/* This file was compiled by Laura Lynn Walsh, Beckman Institute, University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801-2325 (217) 244-6764 lwalsh@nemo.life.uiuc.edu Suggested citations for use of this file are: L. L. Walsh, "Navigating the Brookhaven Protein Data Bank", CABIOS, 10, 551-557 (1994). L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5, Diskette Appendix (1992). This work was begun while the author was working in the laboratory of Dr. Antony R. Crofts at the University of Illinois. LLW was supported by a grant from the National Science Foundations (NSF-DIR90-19063) during the early development of this work. That support is gratefully acknowledged. This file was compiled by Laura Lynn Walsh, NCSA & Beckman Institute University of Illinois. This work was begun while the author L. Walsh, was working as a graduate student in the laboratories of Dr. Antony R. Crofts and Dr. Shankar Subramaniam at the University of Illinois. This development was supported by a grant from the National Science Foundations (NSF-DIR90-19063), during the early development of this work (to A.R. Crofts) and (NSF-ASC-89-02829) (to S. Subramaniam) during the later development. For further enquiries contact lwalsh@aries.scs.uiuc.edu. Suggested citations for use of the text file are: L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5, Diskette Appendix (1992). Date begun: November, 1990 Latest revision: December, 1994 (includes Oct, 1994 update) This file is an annotation of all of the Brookhaven Protein Data Bank files with actual coordinates. (The files beginning with pdb0 have been omitted until full coordinates are available.) The information has been taken from the Brookhaven Protein Data Bank and from original papers by authors listed in those files. Responsibility for the accuracy of the information is LLW's, who would welcome reports of errors and suggestions to extend the usefulness of the information. This information is provided for your use and no warranty about the correctness of the information is made. */ /* References: F. C. Bernstein, T. F. Koetzle, G. J. B., Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, & M. Tasumi, "The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures:, J. Mol. Biol. 112, 535-542 (1977). Macromolecular Structures 1991, Wayne A. Hendrickson & Kurt Wuthrich, eds. and Macromolecular Structures 1992, Wayne A. Hendrickson & Kurt Wuthrich, eds., Current Biology Limited, London, 1991, 1992. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, & D. J. Lipman, "Basic Local Alignment Search Tool", J. Mol. Biol. 215, 403-410 (1990). S. Pascarella & P. Argos, "A Data Bank Merging Related Protein Structures and Sequences", Protein Engineering 5:2, 121-137 (1992). */ /* Description of Entries: The header line begins with the common name for the molecule(s) contained in the file. Commonly accepted names are used if possible, but in several cases, especially the immunoglobulin files, more descriptive names were used. The molecule name is followed by the source of the original sequence. In several cases, a protein is expressed in another organism, such as E. coli, but this is not generally noted. Under the protein name is one or more line(s) indicating the protein's se- quential and structural homologies to other files in the data bank. Infor- mation for sequence homologies was obtained by using the BLAST program blastp (Altschul et al.). Information for structural homologies was obtained from the Pascarella and Argos data files. The unique sequences in the PDB were all BLASTed against each other. Sequences with 50% identity were grouped together and one sequence was chosen as the group "name". Groups with lesser, but still signigicant homologies (a BLAST Poisson score of less than 1.0e-05, a cutoff chosen by inspection) are listed in brackets after the main group name. An entry of *** means that the peptide was too short to produce meaningful results. Structural Classifications: crossed alpha -- helices cross at 70 degree angle up down alpha -- helices cross at 10 degree angle greek alpha -- helices cross at 45 degree angle Greek anti alpha -- globin-like fold a/b open face anti beta -- two layers: alpha, anti beta a/b/a doubly wound para beta -- three layers: alpha, para beta, alpha a/b/a doubly wound anti beta -- three layers: alpha, anti beta, alpha a/b/b doubly wound para beta -- three layers: alpha, para beta, anti beta a/b/c doubly wound para beta -- three layers: alpha, para beta, coil a/b singly wound para beta -- four layers: alpha, para beta, para beta, alpha Greek anti beta -- two layers: anti beta, anti beta Following the sequence homology information is the structural homology group as listed in the database produced by Pascarella and Argos. This information is contained between braces ("{" and "}"). Separate domains of the proteins were classified separately and the residues to which the classification pertains are listed before the structure group name. If the protein was not included in the Pascarella and Argos paper, this information is omitted. The next line occasionally begins with DUP, which indicates that a listing can also be found under name of the other protein or nucleic acid whose coordinates are contained in the file. For example, the Eglin C and subtilisin complex is listed under both headers. The Eglin C listing is marked DUP. The file names from the Brookhaven Protein Data Bank have been abbreviated; only the XXXX part of the pdbXXXX.ent names is used. The columns following the PDB file name indicate the resolution for the x-ray data. If the data entry is derived from NMR data, "NMR" is in this field, since resolution is not applicable in this case. "---" indicates a model structure. A "CA" following the resolution information indicates that the entry contains coordinate information only for the alpha carbons. The body of the entry indicates how many chains are in the "complete" molecule, how many chains are included in the file, and the number of amino acids (or other repeating unit in the case of non-proteins) in each chain [in brackets]. In some cases, I am not able to tell if the protein is multimeric or not (either the literature doesn't mention it or I haven't yet gotten the applicable literature reference). For these files the chain multiplicity is marked "?", e.g., "dimer?" "UNK" in the body of the entry indicates that all or part of the amino acid sequence is unknown. I have listed any co-factors, ions, or other HETATMS present in the data file and included any other information that might help to distinguish that specific entry from another similar entry. I have included any information I had that could help in interpreting the data in the entry. The following abbreviations are used for various HETATMS: 2GP = 2'-guanylic acid 2OG = 2-oxo-glutaric acid AAS = 3-acetoxymercuri-4-aminobenzene sulfonamide ABA = L-alpha-amino-N-butyric acid ACO = acetyl coenzyme A ACT = acetate ion ACY = acetic acid AMP = adenosine monophosphate ADP = adenosine diphosphate ATP = adenosine triphosphate AMX = amidocarboxymethyldethia coenzyme A APU = adenylyl 3'-5' uridine 3' monophosphate AZE = all-trans axerophthene AZM = 5-acetamido-1,3,4-thiadiazole-2-sulfonamide BEN = benzamidine BMT = (4R)-4-[(E)-2-butenyl]-4, N-dimethyl-L-threonine Ca++ = calcium +2 counter ion CBZ = carbobenzoxy group CH3 = methyl group CMS = carbamoyl sarcosine CMX = carboxymethyldethia coenzyme A CTC = 7-chlorotetracycline DEP = diethyl phosphono group DIS = disordered solvent DMF = dimethylformamide DMS = dimethyl sulfoxide DOM = 2'-deoxymaltose DTP = 2'-deoxyadenosine 5'-triphosphate EPE = HEPES N-[2-HYDROXYETHYL]PIPERAZINE-N'-[2-ETHANESULFONIC ACID F6P = fructose-6-phosphate FAD = flavin-adenine dinucleotide FBP = D-fructose-1,6-bisphosphate FDP = fructose-2,6-bisphosphate FEN = N-(4-hydroxyphenyl)all-trans retinamide FES = Fe2-S2 (inorganic) cluster FMN = flavin mononucleotide FOS = [[N-(benzyloxycarbonyl)amino]methyl]phosphinic acid FS3 = iron/sulfur cluster Fe3-S4 FS4 = iron/sulfur cluster Fe4-S4 FUC = fucose G3P = glycerol-3-phosphate GAL = D-galactose GDP = guanosine diphosphate GLC = glucose GMP = guanosine monophosphate GOL = glycerol GTB = S-(p-nitrobenzyl)glutathione GTP = guanosine triphosphate GTS = glutathione sulfonic acid GUA = glutaric acid HEM = protoporphyrin IX HEX = hexane HOH = water HYD = hydroxy group IMD = imidazole ring IPA = isopropyl alcohol ISO = para-isopropylaniline ISP = phosphorylisopropane MAE = maleic acid MAN = alpha-D-mannose MES = N-ethylsulfonic acid morpholine MLE = N-methylleucine MTX = methotrexate MPL = N-methyl-pyridoxal-5'-phosphate MVA = N-methylvaline MZM = 5-acetylamino-4-methyl-1,3,4-thiadozoline-2-sulfonamide NAD = nicotinamide adenine dinucleotide NAP = nicotine adenine dinucleotide phosphate (+) NAG = N-acetyl-D-glucosamine NGA = N-acetyl-D-galactosamine NOP = pyridoxal-5'-phosphate-N-oxide NPL = N-methyl-Ca4-deoxyimino-pyridoxal-5'-phosphate OAA = oxaloacetate OHE = HYDROXYETHYL GROUP PAH = phsophonoacetohydroxamate PHS = phosphono group PLP = pyridoxal-5'-phosphate PMP = pyridoxamine phosphate PO4 = phosphate group PPD = pyridoxal-5'-phosphate-L-aspartate PPE = pyridoxal-5'-phosphate-L-glutamate PRE = prephenate PTP = deoxythymidine-3',5'-bisphosphate REA = retinoic acid RIP = ribose (pyranose form) SBT = 2-butanol SEO = beta-mercaptoethanol SO4 = sulfate SOR = D-sorbitol TFA = trifluoroacetyl group TRS = tromethamine (TRIS buffer) TSA = 1,2,dicarboxy-4-hydroxy-7-oxa-bicyclon-2-ene UDP = uridine 5'-diphosphate UMP = 2'-deoxyuridine 5'-monophosphate XLS = D-xylose XYL = xylitol XYS = cyclic xylose Other abbreviations and symbols: SS(s) = disulfide bond(s) *** = chain did not score high enough in BLAST to classify NMR = structure solved by nuclear magnetic resonance imaging if there are multiple models presented in the file, the viewing program may have difficulty with these files */ XXX look for metal binding crossed anti beta, e.g., Rubredoxin 3-Alpha-20-Beta-Hydroxysteroid Dehydrogenase (Streptomyces hydrogenans) (1hsd.A: 1hsd.A) {a/b/a doubly wound para beta ud/ud} #1hsd 2.6 CA tetramer (a4) - 4 chains given [255]; holo 434 Cro Repressor Protein (Phage 434) (2cro: 2cro [1r69]) {a/a/a doubly wound para alpha cr/cr} [repressor] #2cro 2.35 monomer in solution - 1 chain given [71]; dimer in crystal, but dimerizes differently when bound to DNA; 17 HOHs #3cro 2.5 dimer + dsDNA (a2 + d2) - 4 chains given [71, 20]; 25 HOHs 434 Repressor Protein - N Terminal Domain (Phage 434) (1r69: 1r69 [2cro]) {a/a/a doubly wound para alpha cr/cr} [repressor] #1per 2.5 dimer + dsDNA (a2 + d2) - 4 chains given [69, 20]; 40 HOHs #1pra NMR monomer in solution - 20 models given [69] #1r69 2.0 monomer in solution - 1 chain given [69]; 34 HOHs #1rpe 2.5 dimer + dsDNA (a2 + cd) - 4 chains given [69, 21, 19]; 36 HOHs #2or1 2.5 dimer + dsDNA (a2 + d2) - 4 chains given [69, 20]; 44 HOHs Acetylcholinesterase (Torpedo californica) (1ace: 1ace [1thg]) {domain 1: 4-148,168-234,298-326,401-514: a/b/a doubly wound para beta ud/ud + anti beta} {domain 2: 149-167,235-297: crossed alpha} bow and arrow {domain 3: 327-400,515-534: a/a/a doubly wound para alpha cr/cr} *good for structure picture #1ace 2.8 dimer - 1 chain given [537]; 1 acetylcholine and 71 HOHs; 3 SSs #1acj 2.8 dimer - 1 chain given [537]; 1 1,2,3,4-tetrahydro-9-aminoacridine and 82 HOHs; 3 SSs #1ack 2.8 dimer - 1 chain given [537]; 1 ethyl(3-hydroxyphenyl)dimethyl- ammonium and 86 HOHs; 3 SSs #1acl 2.8 dimer - 1 chain given [537]; 1 decamethonium and 66 HOHs; 3 SSs Acid Proteinase Penicillopepsin (Penicillium janthinellum) (3app: 2apr [3psg] [1smr.A] [1lya.B] [1mpp]) {domain 1: 1-170: multiple anti beta} [ac_prot] {domain 2: 171-323: multiple anti beta} [ac_prot] or XXX not satisfied {domain 1: 1-16,140-183,306-323: c/b open face anti beta + alpha} {domain 2: 17-139: multiple anti beta} reverse s with caps XXX {domain 3: 184-305: Greek anti beta + anti beta} #3app 1.8 monomer [323]; supersedes 2app; 318 HOHs; 1 SS #1apt 1.8 monomer + inhibitor - 2 chains given [323, 4]; 1 isovaleric acid, 1 statine analogue, 1 MAN, and 247 HOHs; 1 SS #1apu 1.8 monomer + inhibitor - 2 chains given [323, 4]; transition state inhibitor; 1 isovaleric acid, 1 statine, 1 ethyl group linked to statine, 1 MAN, and 315 HOHs; 1 SS #1apv 1.8 monomer + inhibitor - 2 chains given [323, 5]; transition state inhibitor; 1 isovaleric acid, 1 2,2-difluoro-3-hydrostatone, 1 n-methylamide, 1 cyclic xylose, 1 dimethylformamide, 1 MAN, and 277 HOHs; 1 SS #1apw 1.8 monomer + inhibitor - 2 chains given [323, 5]; transition state inhibitor; 1 isovaleric acid, 1 2,2-difluorostatine, 1 n-methyl- amide, 1 cyclic xylose, 1 MAN, 1 SO4, and 295 HOHs; 1 SS #1ppl 1.7 monomer + inhibitor - 2 chains given [323, 5]; 1 isovaleric acid, 1 phosphate modified leucine, 1 methyl ester of phe with N re- placed by OP, 1 MAN, 1 cyclic xylose, 1 SO4, and 276 HOHs; 1 SS #1ppm 1.7 monomer + inhibitor - 2 chains given [323, 5]; 1 carbobenzoxy group, 1 phosphate modified leucine, 1 methyl ester of phe with N replaced by OP, 1 MAN, 1 cyclic xylose, 1 SO4, and 306 HOHs; 1 SS Acid Proteinase Rhizopuspepsin (Rhizopus chinensis) (2apr: 2apr [3psg] [1smr.A] [1lya.B] [1mpp]) {domain 1: 1-177: multiple anti beta} [ac_prot] {domain 2: 178-325: multiple anti beta} [ac_prot] or XXX not satisfied {domain 1: 1-13,139-187,307-325: c/b open face anti beta + alpha} {domain 2: 17-139: multiple anti beta} reverse s with caps XXX {domain 3: 188-306: Greek anti beta + anti beta} #2apr 1.8 monomer [325]; supersedes 1apr; 1 Ca++; 373 HOHs; 2 SSs #3apr 1.8 monomer + inhibitor [325, 8]; inhibitor has reduced bond; 344 HOHs; 2 SSs #4apr 2.5 monomer + pepstatin-like renin inhibitor [325, 9]; 1 isovaleric acie, 1 statine, 1 terminal amide, 312 HOHs; 2 SSs #5apr 2.1 monomer + pepstatin-like renin inhibitor [325, 9]; 1 isobutyryl, 1 statine, 1 thioethylamine, 1 Ca++ and 286 HOHs; 2 SSs #6apr 2.5 monomer + pepstatin [325, 6]; 1 isovaleric acid, 2 statine, and 222 HOHs; 2 SSs Mitochondrial Aconitase (Bos taurus) (8acn: 8acn) {domain 1: 2-200: a/b/a doubly wound para beta ud/ud + anti beta + crossed alpha} {domain 2: 201-317: a/b/c doubly wound para beta ud/cr+ anti alpha} {domain 3: 318-519: a/b/c doubly wound para beta ud/ud + anti beta + alpha} {domain 4: 520-754: a/b/b doubly wound para beta ud/cr + coil} [acn+] #8acn 2.0 monomer [754]; 1 FS4 cluster, 1 nitroisocitrate and 321 HOHs #1aco 2.05 monomer? [754]; 1 FS4 cluster, 1 aconitate ion, and 304 HOHs #1nis 2.05 monomer [754]; major inhibitor occupancy form; 1 FS4, 1 nitro- citrate and 290 HOHs #1nit 2.05 monomer [754]; minor inhibitor occupancy form; 1 FS4, 1 SO4, and 290 HOHs Aconitase (Sus scrofa) (6acn: 8acn) {domain 1: 1-200: a/b/a doubly wound para beta ud/ud + anti beta + crossed alpha} {domain 2: 201-317: a/b/c doubly wound para beta ud/cr + anti alpha} {domain 3: 318-519: a/b/c doubly wound para beta ud/ud + anti beta + alpha} {domain 4: 520-754: a/b/b doubly wound para beta ud/cr + coil} [acn] #5acn 2.1 monomer [754]; 1 inactive FS3, 1 SO4, 1 tricarballylic acid, and 407 HOHs #6acn 2.5 monomer [754]; 1 active FS4, 1 SO4, 1 tricarballylic acid, and 407 HOHs #7acn 2.0 monomer [754]; 1 active FS4, 1 isocitrate and 338 HOHs Actin (Oryctolagus cuniculus) (1atn.A: 1atn.A) {domain 1: 0-34,70-136,338-373: a/b/a doubly wound misc beta ud/ud + alpha} {domain 2: 35-69: a/b open face anti beta ud} {domain 3: 137-181,269-337: a/b/a doubly wound misc beta ud/cr} {domain 4: 182-268: a/a open face anti alpha cr + anti beta + alpha} DUP1atn 2.8 monomer + deoxyribonuclease I - 2 chains given [373, 260]; 1:1 indefinitely large multimer; methylated A:H73; 2 NAGs, 1 alpha- D-mannose, 1 ATP, 4 divalent metals, probably Ca++; 2 SSs Actinidin (Actinidia chinensis) (2act: 2act [9pap]) {domain 1: 1-10,111-218: c/b open face anti beta + alpha caps + anti beta} lrdudl - alpha l1, alpha r {domain 2: 11-110: crossed alpha} [pap] XXX not satisfied #2act 1.7 monomer [220]; supersedes 1act; 2 O's bound to SG of C25, 1 ammonium ion, and 272 HOHs; 3 SSs #1aec 1.86 monomer [218]; 1 N-(L-3-trans-carboxyoxirane-2-carbonyl)-L- leucyl)-amido (4-guanido) butane and 268 HOHs; 3 SSs Actinoxanthin (Actinomyces globisporus, number 1131) (1acx: 1acx [2mcm] [1noa]) {Greek anti beta} [acx] XXX Thornton Greek 2 3 loop 1ttg #1acx 2.0 monomer [108]; 2 SSs Acyl Carrier Protein (Escherichia coli B) (1acp: 1acp) {a/a/a doubly wound para alpha ud/cr + coil} #1acp NMR monomer? - 2 models given [77]; model 1 better; some chirality errors in each model Acyl-Coenzyme A Binding Protein (Bos taurus) (2abd: 2abd) {up down mixed alpha} #2abd NMR monomer? - 29 models given [86] #1aca NMR monomer? - 20 models given [86]; 1 ACO and 1 palmitic acid Acylphosphatase (Equus caballus) (1aps: 1aps) {a/b open face anti beta ud} XXX Thornton beta open sandwich #1aps NMR monomer - 5 models given [98] N-ADA (Escherichia coli) (1adn: 1adn) {a/b/a doubly wound anti beta ud/cr + coil} #1adn NMR monomer - 14 models given [92]; 1 Zn++ Adenosine Deaminase (Mus musculus) (1add: 1add) {a/b singly wound para beta + anti alpha cap} [barrel+] #1ada 2.4 CA monomer [352]; 1 6-hydroxy-1,6-dihydro purine nucleoside and 1 Zn #1add 2.4 monomer [349]; 1 1-deaza-adenosine, 1 Zn++, and 110 HOHs Adenylate Kinase Isoenzyme 3 (Bos taurus) (1ak3.A: 1ak3.A [1ake.A] [3adk]) {domain 1: 5-125,159-218: a/b/a doubly wound para beta ud/ud + wedge alphas} {domain 2: 126-158: Greek anti beta + coil} #1ak3 1.9 monomer - 2 chains given [225]; 2 AMPs and 2 SO4s Adenylate Kinase (Escherichia coli) (1ake.A: 1ake.A [1ak3.A] [3adk]) {domain 1: 1-122,156-215: a/b/a doubly wound para beta ud/ud + wedge alphas} {domain 2: 123-155: Greek anti beta + coil} #1ake 1.9 monomer? - 2 chains given [214]; 2 inhibitors: pa,pe-bis(adeno- sine-5') pentaphosphates and 378 HOHs ***1ank 2.0 monomer? - 2 chains given [214]; 2 AMPs, 2 ANPs, and 533 HOHs Adenylate Kinase (Sus scrofa) (3adk: 3adk [1ake.A] [1ak3.A]) {a/b/a doubly wound para beta ud/ud + wedge alpha + greek alpha} [nbd] #3adk 2.1 monomer [195]; supersedes 2adk; 2 SO4s Adipocyte Lipid-Binding Protein (Mus musculus) (1alb: 2hmb [1icm] [1opb.A] [1mdc]) {up down anti beta + anti alpha cap} #1alb 2.5 monomer? [131]; 69 HOHs Agarose (Rhodophycae) #1aga 3.0 sugar polymer; NOT PROTEIN; 2 chains [6, 6]; 3,6-anhydro- L-galactose and GAL Alamethicin (Trichoderma viride) (1amt.A: 1amt.A) {alpha} #1amt 1.5 multimer (an, where n depends on concentration) - 3 chains given [21]; chains include 24 AIBs & 3 PHLs; 2 acetonitriles and 13 methanols; forms voltage-gated ion channels in lipid bilayer; membrane protein Alcohol Dehydrogenase (Equus caballus) (2ohx.A: 2ohx.A [1sdg]) {domain 1: 1-171: multiple anti beta + alpha} {domain 2: 172-341: a/b/a doubly wound para beta ud/ud + crossed alpha} [nbd] {domain 3: 342-374: a/b open face para beta ud} #1adf 2.9 dimer (a2) - 1 chain given [374]; 1 beta-methylene thiazole-4- carboxamide adenine dinucleotide, 2 Zn++s, and 34 HOHs #1adg 2.7 dimer (a2) - 1 chain given [374]; 1 beta-methylene selenazole-4- carboxamide adenine dinucleotide, 2 Zn++s, and 52 HOHs #5adh 2.9 dimer (a2) - 1 chain given [374]; apo; 1 ADP-ribose, 2 Zn++s, 1 2-methyl-2,4-pentanediol and 295 HOHs #6adh 2.9 dimer (a2) - 2 chains given [374]; holo; 2 NADs, 2 dimethyl sulf- oxides, and 2 Zn++s #7adh 3.2 dimer (a2) - 2 chains given [374]; isonicotinamidylated; 2 Zn++s #8adh 2.4 dimer (a2) - 1 chain given [374]; apo; supersedes 4adh; 2 Zn++s and 168 HOHs #2ohx 1.8 dimer (a2) - 2 chains given [374]; holo; 2 NADs, 2 dimethyl sulfoxides, 4 Zn++s, and 459 HOHs #2oxi 2.1 dimer (a2) - 2 chains given [374]; holo; 2 Cu++s, 2 Zn++s, 2 NADs, 2 dimethyl sulfoxides, and 445 HOHs Alcohol Dehydrogenase (Homo sapiens) (1hdx.A: 2ohx.A [1sdg]) {domain 1: 1-171: multiple anti beta + alpha} {domain 2: 172-341: a/b/a doubly wound para beta ud/ud + crossed alpha} [nbd+] {domain 3: 342-374: a/b open face para beta ud} #1hdx 2.5 dimer (a2) - 2 chains given [374]; beta-1 isoenzyme, 47R; 4 Zn++s, 2 NADs, 2 cyclohexanols, 1 Cl-, and 110 HOHs #1hdy 2.5 dimer (a2) - 2 chains given [374]; beta-2 isoenzyme, 47H; 4 Zn++s, 2 NADs, 2 4-iodopyrazole, 1 Cl-, and 105 HOHs #1hdz 2.45 dimer (a2) - 2 chains given [374]; beta-1 isoenzyme R47G mutant; 4 Zn++s, 2 NADs, 1 Cl-, and 83 HOHs #3hud 3.2 dimer (a2) - 2 chains given [374]; beta-1 isoenzyme; 4 Zn++s and 2 NADs Aldolase A (Homo sapiens) (1ald: 1fba.A) {a/b singly wound para beta} [barrel+] #1ald 2.0 tetramer - 1 chain given [363]; Insight-derived coordinates for substrates, glyceraldehyde-3-phosphate, and dihydroxyacetone phosphate, are included in a remark. Aldose Reductase (Homo sapiens) (1ads: 1ads) {a/b singly wound para beta + alpha cap} [barrel+] #1abn 2.4 CA monomer? [315]; C298S mutant; 1 NAP+ and 104 HOHs #1ads 1.6 monomer? [315]; 1 NAP+ and 104 HOHs Aldose Reductase (Sus scrofa) {a/b singly wound para beta + anti beta cap} [barrel+] #1dla 3.0 CA monomer [314] Alkaline Phosphatase (Escherichia coli) (1alk.A: 1alk.A) {a/b/a doubly wound para beta ud/ud + a/b doubly wound anti beta ud/ud + anti beta + alpha} #1alk 2.0 dimer? (a2) - 2 chains given [449]; 4 Zn++s, 2 Mg++s, 2 phos- phates, and 6 HOHs; 4 SSs #1ani 2.5 dimer? (a2) - 2 chains given [446]; D153H, K328H mutant; 6 Zn++s, 5 PO4s, and 270 HOHs; 4 SSs Alpha-1 (synthetic) (1al1: 1dpi) {alpha} #1al1 2.7 tetramer or hexamer - 1 chain given [13]; designed amphiphilic peptide; 1 SO4 Acid Alpha Amylase (Aspergillus niger) (2aaa: 6taa [1cgt]) {domain 1: 1-378: a/b singly wound para beta + anti beta + alpha} [barrel+] {domain 2: 379-476: jelly rell anti beta} #2aaa 2.1 monomer [484]; 2 Ca++s and 350 HOHs; 4 SSs Taka Alpha Amylase (Aspergillus oryzae) (6taa: 6taa [1cgt]) {domain 1: 1-381: a/b singly wound para beta + anti beta + alpha} [barrel] {domain 2: 382-476: double stranded beta cylinder} #2taa 3.0 monomer [478]; supersedes 1taa; 1 Ca++; 4 SSs #6taa 2.1 monomer [478]; 2 Ca++s and 239 HOHs; 4 SSs Beta-Amylase (Glycine max) (1btc: 1btc) {a/b singly wound para beta + alpha + coil loops} [barrel+] #1btc 2.0 monomer? [491]; 4 SEOs, 6 GLCs, 1 SO4, and 318 HOHs #1bya 2.2 monomer [495]; 1 SO4 and 320 HOHs #1byb 1.9 monomer [495]; in 200 MM beta-maltose; 1 SO4, 4 GLCs, and 332 HOHs #1byc 2.2 monomer [495]; in 8 MM beta-maltose; 1 SO4, 4 GLCs, and 332 HOHs #1byd 2.2 monomer [495]; in 100 MM maltal; 1 SO4, 2 DOMs, and 331 HOHs Alpha-1 Antichymotrypsin (Homo sapiens) (2ach.A: 2ach.A [1ova.A] [7api.A] [1pai.A] [1hle.A] [1hle.B]) (2ach.B: 2ach.B [1pai.B] [7api.B]) {domain 1: 24-54,200-290,360-394: a/b/a doubly wound anti beta ud/ud} {domain 2: 55-199,291-358: a/b open face anti beta cr + anti beta} [trypsin++] #2ach 2.7 monomer (cleaved) - 2 chains given [360, 40]; 4 NAGs, 1 MAN, 1 phosphate, and 86 HOHs Alpha-1 Antitrypsin (Homo sapiens) *Cleavage of original monomer yields 3 chains - 3rd "chain" is 1 Cys residue. (7api.A: 7api.A [1ova.A] [2ach.A] [1pai.A] [1hle.A] [1hle.B]) (7api.B: 7api.B [1pai.B] [2ach.B]) {domain 1: 20-53,200-290,359-394: a/b/a doubly wound anti beta ud/ud} {domain 2: 54-199,291-358: a/b open face anti beta cr + anti beta} [trypsin++] #7api 3.0 monomer* - 3 chains given [347, 36, 1]; modified; structural change; tetragonal form 1; supersedes 5api; 7 NAGs, 3 MANs, and 141 HOHs #8api 3.1 monomer* - 3 chains given [347, 36, 1]; modified; structural change; hexagonal form; supersedes 6api; 7 NAGs, 3 MANs, and 159 HOHs #9api 3.0 monomer* - 3 chains given [347, 36, 1]; modified; structural change; tetragonal form 2; 7 NAGs and 3 MANs Alpha-Amylase Inhibitor HOE-467A (Tendamistat) (Streptomyces tendae, 4158) (1hoe: 1hoe) {SS rich Greek anti beta} [hoe] XXX Thornton Greek 2 #2ait NMR monomer - 9 models given [74]; 2 SSs #3ait NMR monomer [74]; energy minimized model using AMBER; 2 SSs #4ait NMR monomer [74]; energy minimized model using FANTOM; 2 SSs #1hoe 2.0 monomer [74]; 23 HOHs; 2 SSs Alpha-Lytic Protease (Lysobacter enzymogenes) (2alp: 2alp [2sga]) {domain 1: 15A-120,232-245: Greek anti beta} 4 loop {domain 2: 120A-231: Greek anti beta} 5 loop [s_prot] XXX Thornton Greek #2alp 1.7 monomer [198]; supersedes 1alp; gaps in numbering; 2 SO4s and 156 HOHs; 3 SSs #1lpr 2.12 monomer + peptide [a + i] - 2 chains given [198, 5]; M192A mutant; 1 methoxysuccinyl, 1 alanine boronic acid, 1 SO4, and 177 HOHs; 3 SSs #2lpr 2.25 monomer + peptide [a + i] - 2 chains given [198, 5]; M192A mutant; 1 methoxysuccinyl, 1 valine boronic acid, 1 SO4, and 180 HOHs; 3 SSs #3lpr 2.15 monomer + peptide [a + i] - 2 chains given [198, 5]; M192A mutant; 1 methoxysuccinyl, 1 norleucine boronic acid, 1 SO4, and 181 HOHs; 3 SSs #4lpr 2.10 monomer + peptide [a + i] - 2 chains given [198, 5]; M192A mutant; 1 methoxysuccinyl, 1 leucine boronic acid, 1 SO4, and 175 HOHs; 3 SSs #5lpr 2.13 monomer + peptide [a + i] - 2 chains given [198, 5]; M213A mutant; 1 methoxysuccinyl, 1 alanine boronic acid, 1 SO4, and 147 HOHs; 3 SSs #6lpr 2.10 monomer + peptide [a + i] - 2 chains given [198, 5]; M213A mutant; 1 methoxysuccinyl, 1 norleucine boronic acid, 1 SO4, and 174 HOHs #7lpr 2.05 monomer + peptide [a + i] - 2 chains given [198, 5]; M213A mutant; 1 methoxysuccinyl, 1 leucine boronic acid, 1 SO4, and 149 HOHs #8lpr 2.25 monomer + peptide [a + i] - 2 chains given [198, 5]; M213A mutant; 1 methoxysuccinyl, 1 phenylalanine boronic acid, 1 sul- fate, and 147 HOHs; 3 SSs #9lpr 2.20 monomer + peptide [a + i] - 2 chains given [198, 5]; 1 methoxy- succinyl, 1 leucine boronic acid, 1 SO4, and 184 HOHs; 3 SSs #1p01 2.0 monomer + inhibitor - 2 chains given [198, 4]; 1 valine boronic acid, 1 tert-butyloxycarbonyl anion, 1 SO4, and 141 HOHs; 3 SSs #1p02 2.0 monomer + inhibitor - 2 chains given [198, 4]; 1 alanine boronic acid, 1 SO4, and 141 HOHs; 3 SSs #1p03 2.15 monomer + inhibitor - 2 chains given [198, 4]; 1 valine boronic acid, 1 SO4, and 141 HOHs; 3 SSs #1p04 2.55 monomer + inhibitor - 2 chains given [198, 4]; 1 isoleucine boronic acid, 1 SO4, and 142 HOHs; 3 SSs #1p05 2.10 monomer + inhibitor - 2 chains given [198, 4]; 1 norleucine boronic acid, 1 SO4, and 146 HOHs; 3 SSs #1p06 2.34 monomer + inhibitor - 2 chains given [198, 4]; 1 phenylalanine boronic acid, 1 SO4, and 163 HOHs; 3 SSs #2p07 2.00 monomer [198]; M192A mutant; supersedes 1p07; 2 SO4s and 166 HOHs; 3 SSs #1p08 2.25 monomer + inhibitor - 2 chains given [198, 4]; M192A mutant; 1 phenylalanine boronic acid, 1 SO4, and 142 HOHs; 3 SSs #1p09 2.20 monomer [198]; M213A mutant; 2 SO4s and 169 HOHs; 3 SSs #1p10 2.25 monomer + inhibitor - 2 chains given [198, 4]; M213A mutant; 1 valine boronic acid, 1 SO4, and 148 HOHs; 3 SSs #1p11 1.93 monomer + inhibitor + peptide - 3 chains given [198, 5, 7]; 1 N- [(2S)-2-(phenoxy(1-R-(N-t-butyl-oxycarbonyl-L-alanyl-L-prolyl)- 1-amino-2-methylpropyl)phosphinyloxy)-propanoyl]-L-alanine methyl ester, 1 truncated inhibitor chain, 1 lactic acid, 1 SO4, and 190 HOHs; 3 SSs #1p12 1.93 monomer + inhibitor - 2 chains given [198, 7]; 1 N-[(2S)-2- (phenoxy(1-R-(N-t-butyl-oxycarbonyl-L-alanyl-L-prolyl)-1-amino- 2-methylpropyl)phosphinyloxy)-propanoyl]-L-alanine methyl ester, 1 lactic acid, 1 SO4, and 183 HOHs; 3 SSs Alzheimer's Beta-Amyloid Precursor Protein (Homo sapiens) (1aap.A: 1aap.A [9pti] [1dtx]) {SS rich a/b open face anti beta + coil} #1aap 1.5 monomer - 2 chains given [58]; protease inhibitor domain; 105 HOHs; 6 SSs DUP1brc 2.5 monomer + trypsin [56, 223]; trypsin variant; 141 HOHs Alzheimer's Amyloid Protein (Homo sapiens) {alphas} #1aml NMR monomer? - 20 models given [40] Amicyanin (Paracoccus denitrificans) (1aaj: 1aaj [1paz] [1plc]) {Greek anti beta} [plasto+] #1aaj 1.8 monomer? [105]; apo; 98 HOHs #1aan 2.0 monomer? [105]; 1 Cu++ and 88 HOHs DUP1mda 2.5 dimer? + electron-transfer partner protein (c2 + a2b2) - 6 chains given [103, 268, 121]; DEL(1-2) variant; 2 O2s and 2 Cu++s; 12 SSs DUP2mta 2.4 monomer + methylamine dehydrogenase + cyt C551 (2c + a2b2 + 2d) - 4 chains given [105, 373, 125, 147]; 2 Os bound to indole ring of L:W57, 1 Cu++, 1 HEM with Fe++, 1 phosphate, and 127 HOHs; 7 SSs Aminopeptidase (Aeromonas proteolytica) {a/b/a doubly wound mixed beta ud/ud + a/b open face para beta ud} #1amp 1.8 monomer? [291]; 2 Zn++s and 356 HOHs; 1 SS Annexin I (Homo sapiens) (1ain: 1ain [1ala]) {domain 1: 6-85: up down anti alpha + alpha} {domain 2: 86-161: up down anti alpha + alpha} {domain 3: 162-246: up down anti alpha + alpha} {domain 4: 247-319: up down anti alpha + alpha} #1ain 2.5 CA monomer? - [314]; 6 Cas; 1 SS Annexin V (Gallus gallus) (1ala: 1ala [1ain]) {domain 1: 3-87: up down anti alpha + alpha} {domain 2: 88-159: up down anti alpha + alpha} {domain 3: 160-246: up down anti alpha + alpha} {domain 4: 247-318: up down anti alpha + alpha} #1ala 2.25 monomer? - [316]; 3 Ca++s and 81 HOHs Annexin V (Homo sapiens) (1avh.A: 1ala [1ain]) {domain 1: 3-87: up down anti alpha + alpha} {domain 2: 88-159: up down anti alpha + alpha} {domain 3: 160-246: up down anti alpha + alpha} {domain 4: 247-320: up down anti alpha + alpha} #1avh 2.3 dimer? - 2 chains given [320]; hexagonal crystal form; 5 Ca++s, 4 SO4s, and 275 HOHs #1avr 2.3 dimer? - 2 chains given [320]; rhombohedral crystal form; 5 Ca++s, 2 SO4s, and 202 HOHs Antennapedia Homeodomain (Drosophila melanogaster) (2hoa: 2hoa [1hdd.C]) {up down anti alpha + crossed alpha} #1ahd NMR monomer + dsDNA - 16 models, 3 chains given [68]; C39S mutant #1hom NMR monomer - 19 models given [68] #2hoa NMR monomer - 20 models given [68]; C39S mutant Antifreeze Polypeptide (Pseudopleuronectes americanus) (1atf: 1atf) {alpha} #1atf --- monomer [37]; non-experimental model Antithrombin III (Bos taurus) {domain 1: 5-231,330-394: a/b/a doubly wound anti beta ud/ud + alphas} {domain 2: 232-329,395-433: a/b/b+open doubly wound anti beta cr/cr + anti beta} #1att 3.2 monomer - 2 chains given [421]; 5 SSs Pokeweed Antiviral Protein Alpha (Phytolacca americana) (1apa: 1apa [2aai.A]) {domain 1: 6-201: a/b doubly wound anti beta ud/cr + anti beta + alpha} {domain 2: 202-266: a/b open face anti beta ud} #1apa 2.3 monomer? [266]; 95 HOHs; 2 SSs Pokeweed Antiviral Protein (Phytolacca americana) (1paf.A: 1apa [2aai.A]) {domain 1: 1-198: a/b doubly wound anti beta ud/cr + anti beta + alpha} {domain 2: 199-262: a/b open face anti beta ud} #1paf 2.5 monomer? - 2 chains given [262]; 87 HOHs; 4 SSs #1pag 2.8 monomer? - 2 chains given [262]; 2 formycins monophosphates and 78 HOHs; 4 SSs Apolipophorin III (Locusta migratoria) (1aep: 1aep) {up down anti alpha} #1aep 2.7 monomer? [161] Apolipoprotein D (Homo sapiens) (2apd: 2apd [1bbp.A] [1hbq]) {up down anti beta + alpha} #2apd --- 1 chain given [169]; non-experimental model; supersedes 1apd; 1 biliverdine IX alpha; 2 SSs Apolipoprotein E (Homo sapiens) (1lpe: 1lpe) {up down anti alpha + crossed alpha} #1le2 3.0 monomer? [144]; LDL receptor binding domain; form E2: R158C mutant #1le4 2.5 monomer? [144]; LDL receptor binding domain; form E4: C112R mutant; 121 HOHs #1lpe 2.25 fragment [144]; LDL receptor binding domain; form E3, most common form; 121 HOHs L-Arabinose Binding Protein (Escherichia coli) (1abe: 1abe) {domain 1: 2-109,256-284: a/b/a doubly wound para beta ud/ud} {domain 2: 110-255,285-306: a/b/a doubly wound para beta ud/ud} [binding] XXX Thornton dw3 #1abe 1.7 monomer [306]; supersedes 1abp; 1 alpha-L-arabinose, 1 beta-L- arabinose, and 227 HOHs #1abf 1.9 monomer [306]; 1 alpha-D-fucose, 1 beta-D-fucose, and 191 HOHs #5abp 1.8 monomer [306]; 1 alpha-D-galactose and 1 beta-D-galactose in same site and 236 HOHs #6abp 1.67 monomer [306]; M108L mutant; 1 alpha-L-arabinose, 1 beta-L-arabi- nose, and 205 HOHs #7abp 1.67 monomer [306]; M108L mutant; 1 alpha-D-fucose, 1 beta-D-fucose, and 193 HOHs #8abp 1.49 monomer [306]; M108L mutant; 2 alpha-D-galactose and 1 beta-D- galactose and 207 HOHs #9abp 1.97 monomer [306]; P254G mutant; 1 alpha-D-galactose and 1 beta- D-galactose in same site; 174 HOHs #1apb 1.76 monomer [306]: P254G mutant; 1 alpha-D-fucose and 1 beta-D- fucose in same site; 168 HOHs #1bap 1.75 monomer [306]; P254G mutant; 1 alpha-L-arabinose and 1 beta- L-arabinose in same site; 154 HOHs ARC Repressor (Salmonella bacteriophage P22) (1arr.A: 1arr.A) {crossed alpha + beta} #1arq NMR dimer (a2) - 16 models of 2 chains each given [53] #1arr NMR dimer (a2) - 2 chains given [53]; minimized average structure Ascorbate Oxidase (Cucurbita pepo medullosa) (1aoz.A: 1aoz.A) {domain 1: 1-128: Greek anti beta} {domain 2: 129-333: double stranded beta cylinder + anti beta} {domain 3: 334-552: double stranded beta cylinder + anti beta} #1aoz 1.9 dimer? (a2) - 2 chains given [552]; 2 NAGs, 3 Cu++s, 1 Cu3-O2, 970 HOHs; 6 SSs #1aso 2.2 dimer? (a2) - 2 chains given [552]; reduced form; 9 Cu++s, 2 OH-s, 2 NAGs, and 969 HOHs; 6 SSs #1asp 2.6 dimer? (a2) - 2 chains given [552]; peroxide form; 9 Cu++s, 2 OH-s, 1 peroxides, 2 NAGs, and 967 HOHs; 6 SSs #1asq 2.3 dimer? (a2) - 2 chains given [552]; azide form; 9 Cu++s, 2 OH-s, 4 azides, 2 NAGs, and 970 HOHs; 6 SSs Asparaginase Type II (Escherichia coli) (3eca.A: 3eca.A) {domain 1: 1-210: a/b/a doubly wound para beta ud/ud + anti betas} {domain 2: 211-326: a/b/a doubly wound para beta ud/ud} #3eca 2.4 tetramer? + Asp substrate - 8 chains given [326, 1]; 410 HOHs; 4 SSs Aspartate Aminotransferase (Escherichia coli) (1asm.A: 1asm.A [7aat.A] [1aat]) {domain 1: 5-70,299-409: a/b/a doubly wound para beta ud/cr + crossed alpha + anti beta} {domain 2: 71-298: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/cr + anti beta} [aat] #1aam 2.8 dimer (a2) - 1 chain given [396]; R292D mutant; 1 pyrodoxal- 5'-phosphate and 1 SO4 #1aaw 2.4 dimer (a2) - 1 chain given [396]; wt; 1 PLP and 3 HOHs #2aat 2.8 dimer (a2) - 1 chain given [396]; K258A mutant; 1 pyridoxamine phosphate; 1 SO4 #3aat 2.8 dimer (a2) - 1 chain given [396]; R386F mutant; 1 PLP and 1 SO4 #1aia 2.20 dimer (a2) - 2 chains given [396]; K258H mutant; 2 PMPs #1aib 2.80 dimer (a2) - 2 chains given [396]; K258H mutant; 2 PMPs and 2 2OGs #1aic 2.40 dimer (a2) - 2 chains given [396]; K258H mutant; 2 PMPs and 2 SO4s #1amq 2.2 dimer (a2) - 1 chain given [396]; 1 PMP and 258 HOHs #1amr 2.1 dimer (a2) - 1 chain given [396]; 1 PMP, 1 MAE, and 264 HOHs #1ams 2.7 dimer (a2) - 1 chain given [396]; 1 PMP and 1 GUA #1ars 1.8 dimer (a2) - 1 chain given [396]; 1 PLP and 127 HOHs #1art 1.8 dimer (a2) - 1 chain given [396]; res 414 is 2 methylaspartate; 1 CH3, 1 PLP and 127 HOHs #1asa 2.4 dimer (a2) - 1 chain given [396]; wt; 1 PLP, 1 MAE, and 16 HOHs #1asb 2.6 dimer (a2) - 1 chain given [396]; D223A mutant; 1 PLP, 1 MAE, and 20 HOHs #1asc 2.4 dimer (a2) - 1 chain given [396]; D223A mutant; 1 NPL and 22 HOHs #1asd 2.2 dimer (a2) - 1 chain given [396]; wt; 1 MPL, 1 MAE, and 127 HOHs #1ase 2.5 dimer (a2) - 1 chain given [396]; wt; 1 NOP, 1 MAE, and 23 HOHs #1asf 2.8 dimer (a2) - 1 chain given [396]; Y226F mutant; 1 PLP and 1 SO4 #1asf 2.8 dimer (a2) - 1 chain given [396]; Y226F mutant; 1 PLP, 1 MAE, and 135 HOHs #1asl 2.60 dimer (a2) - 2 chains given [396]; wt; 2 2-methylaspartyl-pyri- doxal-5'-phosphates and 219 HOHs #1asm 2.35 dimer (a2) - 2 chains given [396]; wt; 2 PLPs, 2 maleic acids, and 223 HOHs #1asn 2.50 dimer (a2) - 2 chains given [396]; wt; 2 PLPs, 2 SO4s, and 228 HOHs #1spa 2.0 dimer (a2) - 1 chain given [396]; D222A mutant; 1 N-(1)- methylated pyridoxal-5'-phosphate-ammonia aldimine and 100 HOHs Cytosolic Aspartate Aminotransferase (Gallus gallus) (1aat: 1aat [1asm.A] [7aat.A]) {domain 1: 2-70,299-412: a/b/a doubly wound para beta (XXX+alpha) ud/cr + crossed alpha + anti beta} {domain 2: 71-298: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/cr + anti beta} [aat+] #1aat 2.8 CA dimer [411]; complex with 2-oxo-glutaric acid Mitochondrial Aspartate Aminotransferase (Gallus gallus) (7aat.A: 7aat.A [1asm.A] [1aat]) {domain 1: 3-70,299-410: a/b/a doubly wound para beta (XXX+alpha) ud/cr + crossed alpha + anti beta} {domain 2: 71-298: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/cr + anti beta} [aat+] #1aka 2.1 dimer (a2) - 2 chains given [401]; K258H mutant; 1 PLP, 1 phos- phate, and 666 HOHs #1akb 2.3 dimer (a2) - 2 chains given [401]; K258H mutant; 1 PPD and 312 HOHs #1akc 2.3 dimer (a2) - 2 chains given [401]; K258H mutant; 1 PPE and 311 HOHs #1ama 2.3 dimer (a2) - 1 chain given [401]; 1 N-pyridroxamine-5'-phospho- alpha-methyl aspartate and 312 HOHs #7aat 1.9 dimer (a2) - 2 chains given [401]; pH 7.5; 2 PLPs and 670 HOHs #8aat 2.3 dimer (a2) - 2 chains given [401]; pH 5.1; 2 PLPs and 600 HOHs #9aat 2.2 dimer (a2) - 2 chains given [401]; pH 7.5; 2 pyridoxamine phos- phate and 620 HOHs #1map 2.45 dimer (a2) - 1 chain given [401]; 1 L-aspartate-pyridoxal-5'- phosphate and 306 HOHs #1maq 2.3 dimer (a2) - 1 chain given [401]; 1 L-glutamate-pyridoxal-5'- phosphate and 303 HOHs #1tar 2.2 dimer (a2) - 2 chains given [401]; 2 PLPs and 228 HOHs #1tas 2.2 dimer (a2) - 2 chains given [401]; 2 PLPs bound to alpha-methyl- aspartic acids and 228 HOHs #1tat 2.2 dimer (a2) - 2 chains given [401]; orthorhombic crystal form; 2 PLPs Aspartate Carbamoyltransferase (Bacillus subtilis) (2at2.A: 2at2.A [8atc.A]) {domain 1: 1-144,270-295: a/b/a doubly wound para beta ud/ud + crossed alpha} {domain 2: 145-269: a/b/c doubly wound para beta ud/ud} #2at2 3.0 CA trimer (a3) - 3 chains given [300] Aspartate Carbamoyltransferase (Escherichia coli) (8atc.A: 8atc.A [2at2.A]) {domain 1: 1-34,131-311: a/b/c doubly wound para beta ud/ud + crossed alpha} {domain 2: 35-130: a/b/a doubly wound para beta ud/ud} [nbd] (8atc.B: 8atc.B) {domain 1: 8-99: a/b open face beta ud} {domain 2: 100-154: c/b open face anti beta cr} #1acm 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; A: R54A and C: R54A mutant; R state; 2 N-(phosphonacetyl)-L-aspartates, 2 Zn++s, and 15 HOHs #2atc 3.0 dodecamer (3[a2b2]) - 2 chains given [305, 152]; unliganded; 1 Zn++; sequences of both subunits differ from all others in this group #8atc 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; R state; 2 N-(phosphonacetyl)-L-aspartate, 2 Zn++s, and 932 HOHs #1at1 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; R state; 2 malonates, 2 phosphonoacetamides, and 2 Zn++s; grown without ligands #2at1 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; R state; 2 phosphonoacetamides, 2 malonates, and 2 Zn++s; grown with ligands #3at1 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; 2 phosphonoacetamides and 2 Zn++s; grown without ligands #4at1 2.6 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; 2 ATPs and 2 Zn++s #5at1 2.6 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; supersedes 7atc; 2 CTPs and 2 Zn++s #6at1 2.6 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; supersedes 4atc; 2 Zn++s #7at1 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; R state; 2 phosphonoacetamides, 2 malonates, 2 Zn++s and 1 ATP #8at1 2.8 dodecamer (3[a2b2]) - 4 chains given [310, 153]; R state; 2 phosphonoacetamides, 2 malonates, 2 Zn++s, and 2 CTPs #1raa 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; fast cooling SA refinement after 250 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rab 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; slow cooling SA refinement after 250 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rac 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; fast cooling SA refinement after 500 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rad 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; slow cooling SA refinement after 500 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rae 2.4 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; fast cooling SA refinement after 750 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1raf 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; slow cooling SA refinement after 750 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rag 2.4 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; fast cooling SA refinement after 1000 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rah 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; slow cooling SA refinement after 1000 steps equilibration; 2 Zn++s, 2 CTPs, and 93 HOHs #1rai 2.5 dodecamer (3[a2b2]) - 4 chains given [310, 153]; T state; final refined structure; 2 Zn++s, 2 CTPs, and 93 HOHs Astacin (Astacus astacus l.) {domain 1: 1-100,176-200: a/b/c+open doubly wound para beta ud/cr} {domain 2: 101-175: anti beta + coil} looks like squashed Ca binding domain #1ast 1.8 monomer? [200]; 1 Zn++ and 182 HOHs; 2 SSs ATX 1A (Anemonia sulcata) (1atx: 1atx [1sh1]) {SS rich c/b/c doubly wound anti beta ud/cr + loop} XXX Thornton SS rich beta #1atx NMR monomer - 8 models given [46]; lowest energy conformation is model 1; has pseudo atoms; 3 SSs Avidin (Gallus gallus) (1avd.A: 1avd.A) {up down anti beta} #1avd 2.7 tetramer (a4) - 2 chains given [128]; 2 biotins, 1 NAG, and 37 HOHs; 2 SSs #1ave 2.8 tetramer (a4) - 2 chains given [128]; apo; 2 NAGs and 21 HOHs; 2 SSs #2avi 3.0 tetramer (a4) - 2 chains given [128]; 2 biotins, 2 NAGs, and 74 HOHs Azurin (Alcaligenes denitrificans) (2aza.A: 2aza.A) {Greek anti beta + alpha} [plasto] XXX Thornton Greek 2 #1aiz 1.8 monomer - 2 chains given [129]; 2 Cds, 4 SO4s, and 239 HOHs; 2 SSs #2aza 1.8 monomer - 2 chains given [129]; supersedes 1aza; oxidized; 2 Cu's, 3 SO4s, and 281 HOHs; 2 SSs #1azb 2.2 monomer - 2 chains given [129]; crystals obtained by removal of Cu from previously-formed crystals of oxidized holo-azurin; 2 Cu++s, 4 SO4s, and 246 HOHs; 2 SSs #1azc 1.8 monomer - 2 chains given [129]; crystals formed from apo- azurin; 2 Cu++s, 2 SO4s, and 246 HOHs; 2 SSs Azurin (Pseudomonas aeruginosa) (4azu.A: 2aza.A) {Greek anti beta + alpha} [plasto] 3 loop #1azn 2.6 monomer - 4 chains given [128]; F114A mutant; 4 Cu++s and 440 HOHs #1azr 2.4 monomer - 4 chains given [128]; N47D mutant; 4 Cus, 1 nitrate, and 324 HOHs #1azu 2.7 monomer [128]; 1 Cu++; 1 SS #2azu 1.9 monomer - 4 chains given [128]; H35L mutant; 4 Cus, 1 nitrate, and 323 HOHs #3azu 2.1 monomer - 4 chains given [128]; H35Q mutant; 4 Cus and 281 HOHs #4azu 1.9 monomer - 4 chains given [128]; pH 5.5; 4 Cu++s, 1 nitrate, and 281 HOHs; 4 SSs #5azu 1.9 monomer - 4 chains given [128]; pH 9.0; 4 Cu++s, 1 nitrate, and 285 HOHs; 4 SSs Bacteriochlorophyll-A Protein (Prosthecochloris aestuarii, strain 2K) (3bcl: 3bcl) {a+b+c/b open face anti beta} #3bcl 1.9 monomer [357]; supersedes 2bcl; many UNK residues; all ASP & ASN are ASX; all GLU & GLN are GLX; 7 bacteriochlorophyll A's and 116 HOHs; membrane associated Bacteriophage Phix174 Coat Protein (Bacteriophage Phix174) (2bpa.1: 2bpa.1) {domain 1: 1-72,228-292,385-426: double stranded beta cylinder} {domain 2: alphas + coil + anti beta} (2bpa.2: 2bpa.2) {double stranded beta cylinder} (2bpa.3: 2bpa.3) {coil} #2bpa 3.0 180mer (60abc) + DNA - 4 chains given [426, 175, 37, 5]; 178 HOHs Bacteriorhodopsin (Halobacterium halobium) (1brd: 1brd) {up down anti alpha} #1bac --- trimer - 1 chain given [248]; non-experimental model; all trans retinal #1bad --- trimer - 1 chain given [248]; non-experimental model; 13-cis retinal #1bct NMR fragment - 14 models of 1 chain given [69]; 163-231; #1bha NMR fragment - 12 models of 1 chain given [71]; 1-71; in SDS #1bhb NMR fragment - 12 models of 1 chain given [71]; 1-71; in methanol- chloroform #1brd 3.5* trimer - 1 chain given [248]; *resolution 3.5 in x and y directions, 10.0 in z; 1 retinal; no turns connecting helices; membrane protein Band 3 (Homo sapiens) {alpha} #1btq NMR monomer fragment [22]; res 405-424; membrane spanning; solubilized in trifluoroethanol; 1 NH2 #1bts NMR monomer fragment [23]; res 436-456; membrane spanning; solubilized in trifluoroethanol; 1 NH2 Barnase (Bacillus amyloliquefaciens) (1brn.L: 1brn.L) {a/b/c doubly wound anti beta ud/cr + crossed alpha} XXX XXX Thornton twisted beta #1ban 2.2 monomer - 3 chains given [110]; S91A mutant; 266 HOHs #1bao 2.2 monomer - 3 chains given [110]; Y78F mutant; 1 Zn++ and 213 HOHs #1bgs 2.6 monomer + inhibitor barstar (ab) - 6 chains given [110, 89]; mutant inhibitor; 199 HOHs #1brg 2.2 monomer - 3 chains given [110]; F7L mutant; 1 Zn++ and 225 HOHs #1brs 2.00 monomer + inhibitor barstar (ab) - 6 chains given [110, 89]; mutant inhibitor; 513 HOHs #1brn 1.76 monomer + ssDNA - 4 chains given [110, 4]; 229 HOHs #1bns 2.05 monomer - 3 chains given [110]; T26A mutant; 224 HOHs #1bsa 2.0 monomer - 3 chains given [110]; I51V mutant; 258 HOHs #1bsb 2.0 monomer - 3 chains given [110]; I76V mutant; 258 HOHs #1bsc 2.0 monomer - 3 chains given [110]; I88V mutant; 237 HOHs #1bsd 2.3 monomer - 3 chains given [110]; I96V mutant; 265 HOHs #1bse 2.0 monomer - 3 chains given [110]; L89V mutant; 187 HOHs #1rnb 1.9 monomer + dinucleotide - 2 chains given [110, 2]; recombinant form; dinucleotide is GC; 1 SO4 and 96 HOHs Barstar (Bacillus amyloliquefaciens) {a/b open face para beta ud + alphas} DUP1bgs 2.6 monomer + barnase (ab) - 6 chains given [89, 110]; C40A, C82A mutant; 199 HOHs DUP1brs 2.00 monomer + barnase (ab) - 6 chains given [89, 110]; C40A, C82A mutant; 513 HOHs #1bta NMR monomer [89]; minimized average structure #1btb NMR monomer - 30 models given [89] Barwin (Hordeum vulgare) (1bw4: 1bw4) {Greek anti beta + wedge alphas} 3 loop XXX #1bw3 NMR monomer? - 20 models given [125]; NOE and dihedral restraints; 3 SSs #1bw4 NMR monomer? - 20 models given [125]; NOE, dihedral, and hydrogen bond restraints; 3 SSs BDS-1 (Anemonia sulcata) (1bds: 1bds) {SS rich c/b/c doubly wound anti beta ud/cr} #1bds NMR monomer [43]; minimized averaged structure; 3 SSs #2bds NMR monomer - 42 models given [43]; 3 SSs Bean Pod Mottle Virus - Middle Component (Bountiful bean) (1bmv.1: 1bmv.1) {double stranded beta cylinder} XXX Thornton Jelly Roll 2 loop (1bmv.2: 1bmv.2) {domain 1: 1-182: double stranded beta cylinder} XXX Thornton Jelly Roll {domain 2: 183-374 double stranded beta cylinder} #1bmv 3.0 120mer + RNA (60ab + r) - 3 chains given [198, 374, 11]; middle component; unusual numbering system Betadoublet (Synthetic) {parallel antibeta sheets} #1btd --- dimer (a2) - 2 chains given [33]; designed protein; 1 SS Bilin Binding Protein (Pieris brassicae) (1bbp.A: 1bbp.A [2apd] [1hbq]) {up down anti beta + alpha} XXX Thornton orthogonal barrel #1bbp 2.0 tetramer (a4) - 4 chains given [173]; 4 biliverdin IX gammas and 424 HOHs Bira Bifunctional Protein (Escherichia coli) (1bia: 1bia) {domain 1: 1-64: crossed alpha + anti beta} {domain 2: 65-270: a/b open face anti beta ud + wedge alpha + a/b/a doubly wound para beta ud/ud} {domain 3: 271-317: up down anti beta} #1bia 2.3 monomer? [321]; 43 HOHs #1bib 2.8 monomer? [321]; 1 biotinylated lysine and 19 HOHs Coagulation Factor X (Bos taurus) (1apo: 1apo) {SS rich c/b open face anti beta ud + anti beta} *** almost a/b open face #1apo NMR fragment - 13 models given [42]; N-terminal domain; 1 HYD; 3 SSs #1ccf NMR fragment - 15 models given [42]; N-terminal domain; 1 HYD; 3 SSs Bombyxin-II (Bombyx mori) {SS rich a/a open face anti alpha cr + 1/2 anti beta} #1bom NMR dimer? - 2 chains given [20, 28]; 3 SSs Bowman-Birk Inhibitor (Phaseolus angularis) (1tab.I: 1pi2 [4mt2]) {SS rich c/b open face anti beta ud} DUP1tab 2.3 monomer + trypsin protease [82, 223]; much of density for inhibitor is missing; 140 HOHs; 10 SSs Bowman-Birk Proteinase Inhibitor (Glycine max) (1bbi: 1pi2 [4mt2]) {domain 1: 1-25,54-71: SS rich c/b open face anti beta cr} {domain 2: 26-53: SS rich c/b open face anti beta cr} #1bbi NMR monomer [71]; minimized average structure; 7 SSs #2bbi NMR monomer - 16 models given [71]; 7 SSs Bowman-Birk Proteinase Inhibitor II (Glycine max) (1pi2: 1pi2 [4mt2]) {domain 1: 2-24,51-63: SS rich c/b open face anti beta cr} {domain 2: 25-50: SS rich c/b open face anti beta cr} #1pi2 2.5 monomer? [63]; 7 SSs Alpha Bungarotoxin (Bungarus multicinctus) source and compound same as 1nbt; seq differs (2abx.A: 2abx.A [1cdt.A] [1nbt.A] [3ebx] [2ctx] [1fas]) {SS rich anti beta} [tox] #1abt NMR monomer? + NACHR peptide - 4 models of 2 chains each [74, 12]; 5 SSs #2abx 2.5 dimer (a2) - 2 chains given [74]; supersedes 1abx; 20 HOHs; 10 SSs Bungarotoxin (Bungarus multicinctus) source and compound same as 2abx; seq differs (1nbt.A: 1nbt.A [1cdt.A] [2abx.A] [3ebx] [2ctx] [1fas]) {SS rich c/b open face anti beta cr} [tox+] #1nbt NMR dimer (a2) - 12 dimeric models given [66]; seq differs from 2abx; some models have wrong chirality for Thr and/or Ile side chains; 10 SSs C5A (Sus scrofa domestica) (1c5a: 1c5a) {a/a/a doubly wound schief para alpha} XXX Thornton cytochrome #1c5a NMR monomer - 41 models given [73]; des-Arg 74; pH 3.0, 25K; 3 SSs C-SRC Kinase (Homo sapiens) {up down anti beta} #1csk 2.5 fragment - 4 chains given [71]; SH3 domain; 8 HOHs Calbindin (Calcium-Binding Protein) (Bos taurus) (4icb: 4icb [2sas] [1osa] [1rro] [4cpv] [1rec]) {crossed alphas + anti beta} XXX Thornton EF hand [ca_bind+] or {a/a/a doubly wound para alpha ud/cr + anti beta} #2bca NMR monomer [76]; D9K form; P43G mutant; minimized average structure #2bcb NMR monomer - 32 models given [76]; D9K form; P43G mutant #1boc NMR monomer - 29 models given [76]; D9K form; A15D, P20G, and P43M mutant #1bod NMR monomer - 24 models given [74]; D9K form; A14DEL, A15D, P20G, N21DEL, and P43M mutant #3icb 2.3 monomer [75]; D9K form; supersedes 2icb; 2 Ca++s, 1 SO4, and 36 HOHs #4icb 1.6 monomer [76]; D9K form; recombinant form with extra N terminal residue; 2 Ca++s and 57 HOHs Calbindin D9K (Sus scrofa) (1cb1: 4icb [2sas] [1osa] [1rro] [4cpv] [1rec]) {greek alphas + anti beta} XXX Thornton EF hand or {a/a/a doubly wound para alpha ud/cr + anti beta} #1cb1 NMR monomer - 13 models given [78] Calcium-Binding Parvalbumin B (Cyprinus carpio) (4cpv: 4cpv [2sas] [4icb] [1osa] [1rro] [1rec]) {a/a/a doubly wound para alpha cr/cr + anti alpha} [ca_bind+] XXX Thornton EF hand #1cdp 1.6 monomer [109]; 2 Cd++s and 73 HOHs #4cpv 1.5 monomer [109]; pI 4.25; 2 Ca++s and 74 HOHs #5cpv 1.6 monomer [109]; supersedes 1cpv, 2cpv, & 3cpv; 2 Ca++s and 74 HOHs Calmodulin (Bos taurus and Rattus rattus) (3cln: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 5-80: crossed alphas + anti beta} [ca_bind] {domain 2: 81-147: crossed alphas + anti beta} [ca_bind] #1cdl 2.2 monomer + peptide - 8 chains given [147, 20]; 16 Ca++s and 270 HOHs #1cdm 2.0 monomer + peptide - 2 chains given [144, 25]; 4 Ca++s and 53 HOHs #2cln --- monomer - 1 chain given [148]; non-experimental model; 4 Ca++s, 2 trifluoperazines, 3 methyls for K115 and 4 HOHs #3cln 2.2 monomer [148]; supersedes 1cln; 4 Ca++s and 69 HOHs #1deg 2.9 monomer [142]; del E84 mutant; 4 Ca++s #1trc 3.6 monomer - 2 chains given [71]; C terminal fragment; residue 129 is D vs. N in 3cln; 4 Ca's Calmodulin (Drosophila melanogaster) (4cln: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 1-80: crossed alphas + anti beta} [ca_bind+] {domain 2: 81-148: crossed alphas + anti beta} [ca_bind+] #2bbm NMR monomer + peptide - 2 chains given [148, 26]; minimized average structure; 4 Ca++s; compact form #2bbn NMR monomer + peptide - 21 models of 2 chains given [148, 26]; 4 Ca++s #4cln 2.2 monomer [148]; 4 Ca++s and 78 HOHs; extended form Calmodulin (Homo sapiens) (1cll: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 4-80: crossed alphas + anti beta} [ca_bind+] {domain 2: 81-148: crossed alphas + anti beta} [ca_bind+] #1cll 1.7 monomer [148]; 4 Ca++s, 1 ethanol, and 139 HOHs Calmodulin (Paramecium tetraurelia) (1osa: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 1-80: crossed alphas + anti beta} [ca_bind+] {domain 2: 81-148: crossed alphas + anti beta} [ca_bind+] #1clm 1.8 monomer [148]; 4 Ca++s and 71 HOHs; possible error in SEQRES records -- SEQRESs same as 1cll, but ATOMs seq as 1osa #1osa 1.68 monomer [148]; 4 Ca++s and 172 HOHs Calmodulin-Dependent Protein Kinase II (Bos taurus) DUP1cdm 2.0 peptide + calmodulin - 2 chains given [25, 144]; 4 Ca++s and 53 HOHs Canavalin (Canavalia ensiformis) (1cau.A: 1cau.A [1cau.B] [1phs]) {domain 1: 44-183,212-224: double stranded beta cylinder} {domain 2: 184-211: crossed alpha} (1cau.B: 1cau.B [1cau.A] [1phs]) {domain 1: 241-386,414-424: double stranded beta cylinder} {domain 2: 387-413: crossed alpha} #1cau 2.3 monomer, cleaved - 2 chains given [181, 184]; proteolyzed; P 21 3 #1cav 2.6 monomer, cleaved - 2 chains given [181, 184]; proteolyzed; P 63 #1caw 2.6 monomer, cleaved - 2 chains given [181, 184]; proteolyzed; R 3 #1cax 2.6 monomer, cleaved - 6 chains given [181, 184]; proteolyzed; C 2 2 21 Canine Parvovirus Viral Protein 2 (Canine Parvovirus, Strain D) (2cas: 2cas) {misc anti beta + anti beta + coil + alpha} #2cas 3.0 60mer (a60) - 1 chain given [548]; empty capsid form; 87 HOHs; 1 SS #2dpv 3.25 60mer (a60) + DNA - 2 chains given [584, 11]; 2 divalent metal ions; 1 SS Carbonic Anhydrase I, Form B (Carbonate Dehydratase) (Homo sapiens) (2cab: 2ca2) {a/b open face anti beta cr + anti beta + coil} [carbonic] #1azm 2.0 monomer [260]; 1 Zn++, 1 AZM, and 180 HOHs #1bzm 2.0 monomer [260]; 1 Zn++, 1 MZM, and 182 HOHs #2cab 2.0 monomer [261]; supersedes 1cab; 1 Zn++ #1czm 2.0 monomer [260]; 1 Zn++, 1 AAS, 5 HG++s, and 178 HOHs #1hcb 1.6 monomer [260]; 1 Zn++, 1 BCT-, and 254 HOHs Carbonic Anhydrase II (Homo sapiens) (2ca2: 2ca2) {a/b open face anti beta cr + anti beta + coil} [carbonic] Protein with 260 residues is recombinant form: it has N-terminal M. #12ca 2.4 monomer [260]; V121A mutant; 1 Zn++, 1 Hg++, and 87 HOHs #1bcd 1.9 monomer [260]; 1 Zn++, 1 trifluoromethane sulphonamide, and 215 HOHs #1bic 1.9 monomer [260]; T200H mutant; 1 Zn++, 1 bicarbonate, 1 methyl Hg+, and 208 HOHs #1ca2 2.0 monomer [259]; supersedes 1cac; 1 Zn++ and 167 HOHs #2ca2 1.9 monomer [259]; 1 Zn++, 1 Hg++, 1 thiocyanate ion, and 172 HOHs #3ca2 2.0 monomer [259]; 1 Zn++, 2 Hg++s, 1 3-mercuri-4-aminobenzene- sulfonamide, and 172 HOHs #4ca2 2.1 monomer [260]; 1 Zn++, 1 Hg++, and 102 HOHs #5ca2 2.1 monomer [260]; T200S mutant; 1 Zn++. 1 Hg++, and 119 HOHs #6ca2 2.5 monomer [260]; V143F mutant; 1 Zn++. 1 Hg++, and 83 HOHs #7ca2 2.4 monomer [260]; V143G mutant; 1 Zn++. 1 Hg++, and 89 HOHs #8ca2 2.4 monomer [260]; V143H mutant; 1 Zn++. 1 Hg++, and 66 HOHs #9ca2 2.8 monomer [260]; V143Y mutant; 1 Zn++. 1 Hg++, and 76 HOHs #1ca3 2.3 monomer [260]; pH 5.7; 1 Zn++, 1 Hg++, and 112 HOHs #4cac 2.2 monomer [260]; form C; pH 6; 1 Zn++ and 160 HOHs #5cac 2.2 monomer [259]; 1 Zn++, 1 hydrogen sulfite, and 152 HOHs #1cah 1.88 monomer [259]; 1 Co++, 1 bicarbonate, and 217 HOHs #1cai 1.8 monomer [260]; E106A mutant; 1 Zn++, 1 SO4, and 206 HOHs #1caj 1.9 monomer [260]; E106D mutant; 1 Zn++, 1 SO4, and 208 HOHs #1cak 1.9 monomer [260]; E106Q mutant; 1 Zn++, 1 SO4, and 209 HOHs #1cal 2.2 monomer [260]; T199A mutant; 1 Zn++ and 209 HOHs #1cam 1.7 monomer [260]; T199A mutant; 1 Zn++, 1 bicarbonate, and 214 HOHs #1can 1.9 monomer [260]; 2 Hg++s, 1 nitrate, and 231 HOHs #1cao 1.9 monomer [260]; 1 Zn++, 1 S, and 230 HOHs #1cay 2.1 monomer [260]; 1 Zn++, 1 acetate, and 217 HOHs #1caz 1.9 monomer [260]; E106Q mutant; 2 Zn++s, 1 acetate, and 210 HOHs #2cba 1.54 monomer [260]; 50mm Tris, 3M ammonium sulfate, pH 7.8; 1 Zn++ and 220 HOHs #2cbb 1.67 monomer [260]; 80mm sodium citrate, 2.4M ammonium sulfate, pH 6.0; 1 Zn++ and 220 HOHs #2cbc 1.88 monomer [260]; 50mm Tris, 3M ammonium sulfate, 0.2 M formate, pH 7.6; 1 Zn++, 1 Hg++, 1 formic acid, and 217 HOHs #2cbd 1.67 monomer [260]; 2.4M ammonium sulfate, 0.3M sodium bisulfite, pH 7.3; 1 Zn++, 1 hydrogen sulfite, and 217 HOHs #2cbe 1.82 monomer [260]; 50mm Tris, 3M ammonium sulfate, 2mm dipicolinate, pH 7.8; 218 HOHs #1cil 1.6 monomer [259]; 1 (4S-trans)-4-(ethylamino)-5,6-dihydro-6-methyl- 4H-thieno(2,3-B)thiopyran-2-sulfonamide-7,7-dioxide, 1 Zn++, and 197 HOHs #1cim 2.1 monomer [259]; 1 (4S-trans)-4-(amino)-5,6-dihydro-6-methyl-4H- thieno(2,3-B)thiopyran-2-sulfonamide-7,7-dioxide, 1 Zn++, 1 methyl Hg+, and 159 HOHs #1cin 2.1 monomer [259]; 1 (4S-trans)-4-(methylamino)-5,6-dihydro-6-methyl- 4H-thieno(2,3-B)thiopyran-2-sulfonamide-7,7-dioxide, 1 Zn++, 1 methyl-Hg+, and 159 HOHs #1cnb 2.35 monomer [259]; H94C mutant; 1 SEO and 135 HOHs #1cnb 2.2 monomer [259]; H94C mutant; 1 Zn++ and 105 HOHs #1cra 1.9 monomer [260]; 1,2,4-triazole; 1 Zn++, 1 Hg++, and 225 HOHs #1cva 2.25 monomer [259]; T199V mutant; 1 Zn++, 1 azide, and 94 HOHs #1cvb 2.4 monomer [259]; T199V mutant; 1 Zn++, 1 SO4, and 95 HOHs #1cvc 2.3 monomer [259]; H94D mutant; 1 Zn++, and 112 HOHs #1cve 2.25 monomer [259]; H119D mutant; 1 Zn++, and 129 HOHs #1cvf 2.25 monomer [259]; H94A mutant; 1 Zn++, and 103 HOHs #1dca 2.2 monomer [260]; T199C mutant; 1 Zn++ and 100 HOHs #1dcb 2.1 monomer [260]; T199C mutant; 1 Zn++ and 93 HOHs #1hca 2.3 monomer [260]; 1 Zn++, 1 Hg++ (bound to C206), and 68 HOHs #1hea 2.0 monomer [260]; L198R mutant; 1 Zn++, 1 Hg++ (bound to C206), and 110 HOHs #1heb 2.0 monomer [260]; L198E mutant; 1 Zn++, 1 Hg++ (bound to C206), and 107 HOHs #1hec 2.0 monomer [260]; L198H mutant; 1 Zn++ and 91 HOHs #1hed 2.0 monomer [260]; L198A mutant; 1 Zn++, 2 Hg++s (bound to C206), and 107 HOHs #1hva 2.3 monomer [260]; H94C mutant; 38 HOHs #1mua 1.7 monomer [256]; DEL(1-3), P202A mutant; 1 Zn++, 1 Hg++, and 91 HOHs #1ray 1.8 monomer [260]; 1 Zn++, 1 azide, and 217 HOHs #1raz 1.9 monomer [260]; 1 Zn++, 1 bromine, and 218 HOHs #1rza 1.9 monomer [260]; 1 Co++, 1 dioxygen, and 218 HOHs #1rzb 1.8 monomer [260]; pH 6.0; 1 Co++, 1 SO4, and 216 HOHs #1rzc 1.9 monomer [260]; 2 Cu++s, 1 dioxygen, and 216 HOHs #1rzd 1.9 monomer [260]; 1 Mn++, 1 SO4, and 216 HOHs #1rze 1.9 monomer [260]; 1 Ni++, 1 SO4, and 217 HOHs Carboxypeptidase A (Bos taurus) (2ctb: 2ctb [1cpb] [1pba]) {a/b/a doubly wound mixed beta ud/ud} [cpa] XXX Thornton dw1 (2ctb) #1cbx 2.0 monomer [307]; 1 L-benzylsuccinate inhibitor, 1 Zn++, and 178 HOHs; 1 SS #3cpa 2.0 monomer + peptide - 2 chains given [307, 2]; supersedes 1cpa; 1 glycyl-L-tyrosine; 1 Zn++; 1 SS #4cpa 2.5 monomer + potato inhibitor + Gly - 3 chains [307, 38, 1]; super- sedes 1cpa; 1 Zn++; 4 SSs #5cpa 1.54 monomer [307]; 1 Zn++ and 192 HOHs; 1 SS #6cpa 2.0 monomer [307]; 1 O-[[(1R)-[[N-phenylmethoxycarbonyl-L-alanyl] amino]ethyl]hydroxyphosphinyl-L-3-phenyllactate, 1 Zn++, and 149 HOHs; 1 SS #7cpa 2.0 monomer [307]; 1 O-(((1R)-((N-(phenylmethoxycarbonyl)-L-phenyl- alanyl)amino)isobutyl)hydroxyphosphinyl)-L-3-phenyllactate, 1 Zn++, and 222 HOHs; 1 SS #8cpa 2.0 monomer [307]; 1 O-(((1R)-((N-(phenylmethoxycarbonyl)-L-alanyl) amino)methyl)hydroxyphosphinyl)-L-3-phenyllactate, 1 Zn++, and 254 HOHs; 1 SS #1cps 2.25 monomer [307]; 1 [L-(-)-2-carboxy-3-phenylpropyl]methyl-sulfodi- imine, 1 Zn++, and 122 HOHs; 1 SS #2ctb 1.5 monomer [307]; 1 Zn++ and 218 HOHs; 1 SS #2ctc 1.4 monomer [307]; 1 L-phenyl lactate, 1 Zn++, and 181 HOHs; 1 SS Carboxypeptidase A (Sus scrofa) (1pca: 2ctb [1cpb] [1pba]) {domain 1: 4A-99A: a/b open face anti beta ud} {domain 2: 1-308: a/b/a doubly wound mixed beta ud/ud + coil} #1pca 2.0 monomer? [403]; zymogen; 1 Zn++, 1 citrate, and 294 HOHs; 1 SS Potato Carboxypeptidase A Inhibitor (Solanum suberosum) (4cpa.I: 4cpa.I) {SS rich c/b open face anti beta ud} DUP4cpa 2.5 inhibitor + carboxypeptidase A - 2 chains [38, 307]; supersedes 1cpa; 1 Zn++ Carboxypeptidase B (Bos taurus) (1cpb: 1cpb [2ctb] [1pba]) {a/b/a doubly wound para beta ud/ud + coil} #1cpb 2.8 CA monomer [306]; fraction II; some of helices have flattened shape; very close approach of two parts of chain; 3 SSs Carboxypeptidase B (Sus scrofa domestica) (1pba: 1pba [2ctb] [1cpb]) {a/b open face anti beta ud} #1pba NMR monomer - 19 models given [81]; procarboxypeptidase B - activa- tion domain D-Alanyl-D-Alanine Carboxypeptidase/Transpeptidase (Streptomyces r61) (2pte.E: 2pte.E) {domain 1: 14-147,268-353: a/b/a doubly wound para beta ud/ud} {domain 2: 148-267: a/a/c doubly wound para alpha ud/cr} #1pte 2.8 CA seq uncertain [~353]; no SEQRES records #2pte --- monomer? + peptide - 2 chains given [349, 3]; non-experimental model Capsular Polysaccharide (Escherichia coli) #1cap 3.0 monomer [12]; from mutant; NOT PROTEIN Cardiotoxin CTX IIB (Naja mossambica mossambica) (2ccx: 1cdt.A [3ebx] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich anti beta} [tox+] XXX B&T 28c #2ccx NMR monomer - 20 models given [60]; 4 SSs Cardiotoxin V (Naja naja atra) (1cvo: 1cdt.A [3ebx] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich anti beta} [tox+] XXX B&T 28c #1cvo NMR monomer? - 2 models given [62]; 4 SSs Cardiotoxin V4 (Naja mossambica mossambica) (1cdt.A: 1cdt.A [1nbt.A] [2abx.A] [3ebx] [2ctx] [1fas]) {SS rich anti beta} [tox+] XXX B&T 28c #1cdt 2.5 dimer (a2) - 2 chains given [60]; 2 phosphates and 48 HOHs; 8 SSs Catabolite Gene Activator Protein (Escherichia coli) (3gap.A: 3gap.A) {domain 1: 1-136: double stranded beta cylinder + up down anti alpha + crossed alpha} {domain 2: 137-205: a/b open face anti beta cr + crossed alphas} [gap] #1cgp 3.0 dimer + dsDNA (a2 + d2) - 4 chains given [205, 31]; 2 cyclic AMPs #2gap --- dimer + ssDNA (a2 + d) - 3 chains given [208, 48]; model #3gap 2.5 dimer (a2) - 2 chains given [209]; supersedes 1gap; chains have different configurations; 2 c-AMPs and 126 HOHs Catalase (Penicillium vitale) (4cat: ???) {domain 1: 1-53: alpha + coil} {domain 2: 54-133,189-422: up down anti beta + coil} {domain 3: 134-188,423-503: up down anti alphas} {domain 4: 504-659: a/b/a doubly wound para beta ud/ud} [cat?] #4cat 3.0 monomer? [659]; all residues UNK; 1 HEM with Fe+++ Catalase (Bos taurus) (7cat.A: 7cat.A) {domain 1: 3-66: alpha + coil} {domain 2: 67-148, 205-432: up down anti beta + coil} {domain 3: 149-204,433-500: up down anti alpha + crossed alpha} [cat] #7cat 2.5 tetramer (a4) - 1 chain given [506]; supersedes 3cat; 1 HEM with Fe+++, 1 NADPH, and 50 HOHs #8cat 2.5 tetramer (a4) - 2 chains given [506]; supersedes 3cat; 2 HEMs with Fe+++s, 2 NADPHs, and 98 HOHs Cathepsin D (Homo sapiens) (1lya.A: 1smr.A [3psg] [1lya.B] [1mpp] [2apr]) (1lya.B: 1lya.B [3psg] [1smr.A] [1mpp] [2apr]) {domain 1: 1-13,150-199,329-346: c/b open face anti beta + alpha} {domain 2: 14-149: 3 layer anti beta} reverse s with caps XXX {domain 3: 200-328: Greek anti beta + anti beta} #1lya 2.5 monomer (cleaved, ab) - 4 chains given [97, 241]; 6 NAGs, 4 MANs, and 46 HOHs; 8 SSs #1lyb 2.5 monomer (cleaved, ab) + inhibitor - 6 chains given [97, 241, 6]; 6 NAGs, 4 MANs, 2 isovaleric acids, 4 statines, and 44 HOHs; 8 SSs CD2 (Homo sapiens) XXX remove? (1cdb: 1cdb) {Greek anti beta} #1cdb NMR monomer? - 18 models given [105]; adhesion domain CD2 (Saccharomyces cerevisiae) (1d66.A: 1d66.A) {domain 1: 8-41: 1/2 X para alpha} {domain 2: 42-64: 2 X (metal rich alpha + coil)} #125d NMR monomer (fragment) - 22 structures given [43]; GAL4 binding domain; model 9 has fewest constraint violations; 2 Cds #1d66 2.7 dimer + dsDNA (a2 + d2) - 4 chains given [66, 19]; GAL4 binding domain; 4 Cds and 51 HOHs CD4 (Homo sapiens) (3cd4: 3cd4) {domain 1: 1-96: Greek anti beta} [igb] XXX Thornton Greek 2 {domain 2: 97-178: Greek anti beta} [igb] XXX Thornton Greek 2 #3cd4 2.2 monomer [182]; supersedes 2cd4; N-terminal fragment; 30 HOHs; 2 SSs #1cdh 2.3 monomer [178]; supersedes 1cd4; N-terminal fragment, domains 1 and 2; type I crystal form; 86 HOHs; 2 SSs #1cdh 2.9 monomer [179]; supersedes 1cd4; 0T insertion; N-terminal fragment, domains 1 and 2; type II crystal form; 2 SSs CD4 (Rattus rattus) (1cid: 1cid) {domain 3: 1-105: Greek anti beta} {domain 4: 106-202: Greek anti beta} #1cid 2.8 monomer? [177]; domains 3 and 4; 1 SO4 and 14 HOHs; 1 SS CD8 (Homo sapiens) (1cd8: 1cd8) {Greek anti beta} XXX Thornton Greek 2 #1cd8 2.6 dimer (a2) - 1 chain given [114]; N-terminal fragment; soluble form; 1 SO4 and 23 HOHs; 1 SS CD40 Ligand (Mus musculus) (1cda.A: 1cda.A) {double stranded beta cylinder} #1cda --- trimer (a3) - 3 chains given [146]; model based on 1tnf; 3 SSs CD59 (Homo sapiens) {SS rich a/b/b+c doubly wound anti beta cr/ud} #1cdq NMR monomer - 20 models given [77]; 5 SSs #1cdr NMR monomer - 10 models given [77]; 2 NAGs and 1 FUC; 5 SSs #1cds NMR monomer - 10 models given [77]; 2 NAGs; 5 SSs #1erg NMR monomer [70]; minimized average structure; 5 SSs #1erh NMR monomer - 10 models given [70]; 5 SSs Cellobiohydrolase I (Trichoderma reesei) (1cbh: 1cbh) {SS rich Greek anti beta + anti alpha + coil} XXX really two large curved anti beta sheets #1cbh NMR fragment [36]; minimized averaged structure; C-terminal domain; 2 SSs #2cbh NMR fragment - 41 models given [36]; C-terminal domain; 2 SSs #1cel 1.81 fragment - 2 chains given [434]; catalytic domain; 2 NAGs, 2 IBZs, 2 GLCs, 1 Ca++, and 529 HOHs; 20 SSs Cellobiohydrolase II Core Protein (Trichoderma reesei) (3cbh: 3cbh [1tml]) {half of a/b singly wound para beta + anti alpha + crossed alpha + coil} #3cbh 2.0 CA monomer [365]; 2 SSs Charybdotoxin (Leiurus quinquestriatus hebraeus) (2crd: 2crd) {SS rich a/b open face anti beta} #2crd NMR monomer - 12 models given [37]; 3 SSs Che-Y (Escherichia coli) {a/b/a doubly wound para beta ud/ud} #1chn 1.76 monomer [128]; 1 Mg++ and 71 HOHs #3chy 1.66 monomer [128]; has commented models for a phosphate and a Mg ion not seen in density; 3 SO4s and 147 HOHs Che-Y (Salmonella typhimurium) (3chy: 3chy) {a/b/a doubly wound para beta ud/ud} *good for structure picture XXX Thornton dw1 #2chy 2.7 CA monomer [128]; S56C mutant; 3 other differences from 2chy Chloramphenicol Acetyltransferase - Type III (Escherichia coli) (3cla: 3cla) {a/b/c doubly wound mixed beta ud/ud + a/b open face anti beta cr + anti beta + alpha} [cla] #1cia 2.5 trimer (a3) - 1 chain given [213]; H195Q mutant; 2 Co++s, 1 beta- mercaptoethanol, and 124 HOHs #1cla 2.34 trimer (a3) - 1 chain given [213]; S148A mutant; 1 chlor- amphenicol, 2 Co++s, and 137 HOHs #2cla 2.35 trimer (a3) - 1 chain given [213]; D199N mutant; 2 Co++s and 104 HOHs #3cla 1.75 trimer (a3) - 1 chain given [213]; 1 chloramphenicol, 2 Co++s, and 204 HOHs #4cla 2.0 trimer (a3) - 1 chain given [213]; L160F mutant; 1 chloramphen- icol, 2 Co++s, and 203 HOHs Chloromuconate Cycloisomerase (Alcaligenes eutrophus, strain JMP134) (1chr.A: 1chr.A [1mle] [2mnr]) {domain 1: 1-119+360-370: a/b open face anti beta + alphas} {domain 2: 120-359: a/b singly wound para beta + anti beta} #1chr 3.0 dimer? (a2) - 2 chains given [370]; 2 Mn++s and 1 Cl- Cholera Toxin (Vibrio cholerae) (1chb.D: 1lts.D) {SS rich a/b misc anti beta} or XXX Cynthia look {domain 1: 1-24,80-108: a/b open face anti beta ud} {domain 2: 25-79: a/b open face anti beta ud} or {a/b/a doubly wound misc beta ud/ud} #1chb 2.2 hexamer (ab5) - 5 chains given [104]; b-pentamer only; 6 D-galac- toses, 5 N-acetyl-D-galactoseamines, 5 sialic acids, 1 GLC, and 284 HOHs; 5 SSs DUP1tet 2.3 fragment + antibody dimer (ab) - 3 chains given [15, 216, 210]; 1 citrate and 151 HOHs; 4 SSs Cholesterol Oxidase (Brevibacterium sterolicum) (3cox: 3cox) {domain 1: a/b misc para beta} {domain 2: Greek anti beta} {domain 3: misc anti beta} or {domain 1: 5-156,215-320,384-402,442-510: a/b/b doubly wound para beta + crossed alpha + anti betas + coil} {domain 2: 157-214,321-383,403-441: a/b open face anti beta ud + para alpha} #3cox 1.8 monomer [507]; supersedes 1cox; 1 FAD and 453 HOHs #1coy 1.8 monomer [507]; 1 3-beta-hydroxy-5-androsten-17-one, 1 FAD and 424 HOHs Chondroitin-4-Sulfate (Bos taurus) #1c4s 3.0 1 chain [4]; NOT PROTEIN; 2 D-glucuronic acids, 2 2-deoxy-2-acet amido-beta-D-galactose-4-sulfates, 6 Na+s, and 30 HOHs #2c4s 3.0 1 chain [4]; NOT PROTEIN; 2 D-glucuronic acids, 2 2-deoxy-2-acet- amido-beta-D-galactose-4-sulfates, 2 Ca++s, and 14 HOHs Chorismate Mutase (Bacillus subtilis) {a+c/b open face anti beta ud} #1com 2.2 trimer (a3) - 12 chains given [127]; 9 PREs and 503 HOHs; more than 15000 atoms in file Chymosin B (Bos taurus) (4cms: 3psg [1smr.A] [1lya.B] [1mpp] [2apr]) {domain 1: 1-175: multiple anti beta} [ac_prot] {domain 2: 176-323: multiple anti beta} [ac_prot] or XXX {domain 1: -2-9,145-183,309-326: c/b open face anti beta ud} {domain 2: 10-144: 3 layer Greek anti beta} {domain 3: 145-183,309-326: Greek anti beta + anti betas + alpha} [ac_prot] #1cms 2.3 monomer [323]; 297 HOHs; 3 SSs #3cms 2.0 monomer [323]; V111F mutant; 145 HOHs; 3 SSs #4cms 2.2 monomer [323]; 131 HOHs; 3 SSs Chymotrypsin (Bos taurus) (2cga.A: 2cga.A [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1sgt] [1hne.E]) {domain 1: 1-29,118-231: Greek anti beta + alpha} XXX check again {domain 2: 30-117,232-245: Greek anti beta} [s_prot] #1acb 2.0 monomer + Eglin-C inhibitor - 2 chains given [245, 70]; alpha; 142 HOHs; 5 SSs #2cga 1.8 monomer - 2 chains given [245]; alpha; zymogen; 329 HOHs #1cgi 2.3 monomer + human pancreatic secretory inhibitor, var. 3 - 2 chains given [245, 56]; alpha; zymogen; 52 HOHs; 8 SSs #1cgj 2.3 monomer + human pancreatic secretory inhibitor, var. 4 - 2 chains given [245, 56]; alpha; zymogen; 56 HOHs; 8 SSs #1cho 1.8 monomer + ovomucoid 3rd domain inhibitor - 2 chains given [245, 56]; alpha; 221 HOHs; 8 SSs #2cha 2.0 monomer [245]; 1 p-toluene sulfonate bound to S195; EXC for excised residues; alpha; 50 HOHs; 5 SSs #4cha 1.68 monomer - 2 chains given [245]; alpha; EXC for excised residues; 85 HOHs; 10 SSs #5cha 1.67 "dimeric structural unit" (a2) - 2 chains given [245]; alpha; supersedes 3cha; EXC for excised residues; 247 HOHs; 10 SSs #6cha 1.8 "dimeric structural unit" (a2) - 2 chains given [245]; alpha; 2 phenylethane boronic acids and 185 HOHs; 10 SSs #1chg 2.5 monomer [245]; alpha; zymogen; 5 SSs #1gcd 1.9 monomer [245]; gamma; ph 5.6, temp 90K; 3 SO4s, 1 DEP, and 278 HOHs; 5 SSs #2gch 1.9 monomer [245]; supersedes 1gch; gamma; 151 HOHs; 5 SSs #3gch 1.9 monomer [245]; gamma; 1 trans-o-hydroxy-alpha-methyl cinnamate and 76 HOHs; 5 SSs #4gch 1.9 monomer [245]; gamma; 1 p-diethylamino-o-hydroxy-alpha-methyl cinnamate and 73 HOHs; 5 SSs #5gch 2.7 monomer [245]; gamma; photolysis product of inhibited molecule; 78 HOHs; 5 SSs #6gch 2.1 monomer [245]; gamma; 1 1,1,1-trifluoro-3-acetamido-4-phenyl butan-2-one and 188 HOHs; 5 SSs #7gch 1.8 monomer [245]; gamma; 1 1,1,1-trifluoro-3-((N-acetyl)-L-leucyl- amido)-4-phenyl-butan-2-one and 99 HOHs; 5 SSs #8gch 1.6 monomer + peptide - 2 chains given [245, 3]; gamma; -183 deg C; 1 Gly-Ala-Trp, 4 SO4s, and 346 HOHs; 5 SSs #1gct 1.6 monomer + inhibitor - [245, 4]; gamma; excised residues of monomer form 3 separate chains, but same chain name is used; A; 1 SO4, 164 HOHs; pH 7.0; 5 SSs #2gct 1.8 monomer + inhibitor - [245, 5]; gamma; pH 2.0; chains as for 1gct; A; 2 SO4s, 131 HOHs; 5 SSs #3gct 1.6 monomer + inhibitor - [245, 5]; gamma; chains as for 1gct; A; 1 SO4, 141 HOHs; pH 10.5; 5 SSs #1gha 2.2 monomer + peptide - 2 chains given [245, 4]; gamma; 1 SO4, 1 IPA, and 173 HOHs; 5 SSs #1ghb 2.0 monomer + peptides - 3 chains given [245, 3, 2]; gamma; 5 HEXs, 3 IPAs, and 309 HOHs; 5 SSs #1gmc 2.2 monomer + cleavage product - 2 chains given [245, 4]; gamma; excised residues of zymogen form 3 chains in mature form, only one chain name used; 97 HOHs; 5 SSs #1gmd 2.2 monomer + cleavage product - 2 chains given [245, 5]; gamma; excised residues of zymogen form 3 chains in mature form, only one chain name used; 7 HEXs and 130 HOHs; 5 SSs #1gmh 2.1 monomer [245]; 1 ISP, 2 SO4s, and 102 HOHs; 5 SSs Chymotrypsin Inhibitor (Psophocarpus tetragonolobous) {6 anti beta pairs on cube faces} crossed XXX 1tie #1wbc 2.95 monomer [183]; 56 HOHs Chymotrypsin Inhibitor 2 (Hordeum vulgare, hiproly strain) (2ci2.I: 2ci2.I [1egl]) {a/b/c doubly wound para beta ud/ud + anti beta} [eglin] #2ci2 2.0 monomer [83]; 64 HOHs #3ci2 NMR monomer - 20 models given [66]; truncated from 2ci2, E78Q mutant #1coa 2.2 monomer [64]; I76V mutant; truncated form; 32 HOHs DUP2sni 2.1 monomer + protease subtilisin - 2 chains given [83, 275]; 2 Ca++s and 168 HOHs #1ypa 2.0 monomer [64]; S31A, E33A, E34A mutant; 53 HOHs #1ypb 2.0 monomer [64]; S31G, E33A, E34A mutant; 52 HOHs #1ypc 1.7 monomer [64]; E33A, E34A mutant; 56 HOHs Citrate Synthase (Gallus gallus) (1csc: 1csc) {domain 1: 1-270,394-433: up down anti alpha + crossed alpha + anti beta} {domain 2: 271-393: Greek anti alpha} [cts+] XXX check or {domain 1: 1-270,394-433: a/a/a three layer alpha: crossed/anti/anti + anti beta + alpha} {domain 2: 271-393: up down anti alpha} B&T28k + crossed alpha #1csc 1.7 dimer (a2) - 1 chain given [433]; seq inferred from Sus scrofa and electron density - four UNK residues; 1 L-malate, 1 carboxy- methyl ACO, and 101 HOHs #2csc 1.7 dimer (a2) - 1 chain given [433]; seq as 1csc; 1 D-malate, 1 car- boxymethyl ACO, and 101 HOHs #3csc 1.9 dimer (a2) - 1 chain given [433]; seq as 1csc; 1 L-malate, 1 ACO, and 101 HOHs #4csc 1.9 dimer (a2) - 1 chain given [433]; seq as 1csc; 1 D-malate, 1 ACO, and 101 HOHs #5csc 2.8 dimer (a2) - 2 chains given [433]; seq as 1csc; open form #1csh 1.6 dimer (a2) - 1 chain given [435]; 1 AMX, 1 OAA, and 145 HOHs #1csi 1.7 dimer (a2) - 1 chain given [435]; 1 CMX, 1 OAA, and 143 HOHs #3cts 1.7 dimer (a2) - 1 chain given [433]; 1 ACO, 1 citrate, and 108 HOHs; residues all UNK #5cts 1.9 dimer (a2) - 1 chain given [433]; seq as 1csc; 1 OAA, 1 carboxymethyl ACO, and 101 HOHs; same form as 2cts, presumably monoclinic, closed; protruding N-terminus in contact with neighboring dimer #6cts 2.5 dimer (a2) - 1 chain given [433]; seq as 1csc; 1 citryl-thio- ether-coenzyme A and 101 HOHs Citrate Synthase (Sus scrofa) (2cts: 1csc) {domain 1: 1-270,394-433: a/a/a three layer alpha: crossed/anti/anti + anti beta + alpha} XXX {domain 2: 271-393: up down anti alpha} B&T28k + crossed alpha [cts] #1cts 2.7 dimer (a2) - 1 chain given [437]; A32V variant; 1 citrate ion #2cts 2.0 dimer (a2) - 1 chain given [437]; 1 ACO, 1 citrate, and 95 HOHs; monoclinic form (closed) #4cts 2.9 dimer (a2) - 2 chains given [437]; A32V variant; 2 OAAs and 96 HOHs; tetragonal form (open) Clara Cell 17 KDA Protein (Rattus rattus) (1ccd: 1utg) {a/a open face anti alpha ud} [utg] XXX Cynthia look #1ccd 3.0 dimer (a2) - 1 chain given [77]; 1 SO4 Clupeine Z (Atlantic herring) (7ins.G: 7ins.G) {unknown} DUP7ins 2.0 monomer + insulin dodecamer (p + 6ab) - 7 chains given [31, 21, 30]; residues of monomer are not all connected; 1 Zn++, 3 m-cre- sols, and 109 HOHs Alpha Cobratoxin (Naja naja siamensis) (2ctx: 2ctx [1cdt.A] [1nbt.A] [2abx.A] [3ebx] [1fas]) {SS rich anti beta} [tox] or {SS rich c/b/c doubly wound anti beta ud/ud + alpha + coil} XXX Cynthia #1ctx 2.8 monomer [71]; 5 SSs #2ctx 2.4 monomer [71]; 31 HOHs; 5 SSs Cobrotoxin (sic) (Naja naja atra) {SS rich anti beta} [tox] #1cre NMR monomer [60]; minimized average structure; 4 SSs #1crf NMR monomer - 12 models given [60]; 4 SSs Coiled Serine (Synthetic) (1cos.A: 1cos.A) {up down anti alpha} #1cos 2.1 trimer - 3 chains given [31]; 3 terminal amides and 33 HOHs Colicin A (Escherichia coli) (1col.A: 1col.A) {Greek anti alpha} XXX check -- Thornton calls this a globin #1col 2.4 monomer - 2 chains given [204]; C-terminal membrane pore forming domain; 83 HOHs Collagen (Synthetic) (1clg.A: 1clg.A) {para coiled coil} #1bbe --- trimer (a3) - 3 chains given [14]; non-experimental model "1"; poly(GPP); 3 ACEs and 3 NMEs #1bbf --- trimer (a3) - 3 chains given [14]; non-experimental model "2"; A: poly(PPG), B: poly(GPP), C: poly(PGP); 3 ACEs and 3 NMEs #1clg --- trimer (a3) - 3 chains given [38]; non-experimental model; poly(GPP); 3 N-methylamides #2clg --- trimer (a3) - 3 chains given [38]; non-experimental model; poly(GP-Hyp); 3 N-methylamides #4clg --- trimer (a3) - 15 chains given [38]; non-experimental model; poly(GP-Hyp); 15 N-methylamides Collagen-like Peptide (Synthetic) #1cag 1.85 trimer (a3) - 3 chains given [30]; 6 ACYs and 85 HOHs Concanavalin A (Canavalia ensiformis) (2ctv.A: 2ctv.A [1lec] [1lte] [2ltn.A] [2ltn.B]) {Greek anti beta} [ltn] #1cn1 3.2 dimer (a2) - 2 chains given [237]; demetallized; residues 187-190 are ATVS vs. TVSA in 2cna #2cna 2.0 dimer or tetramer (a2 or a4) - 1 chain given [237]; 1 Mn++, 1 Ca++, and 4 HOHs #3cna 2.4 dimer or tetramer (a2 or a4) - 1 chain given [237]; residues 187-190 are ATVS vs. TVSA in 2cna; 1 Mn++, 1 Ca++, and 4 HOHs #4cna 2.9 dimer or tetramer (a2 or a4) - 4 chains given [237]; seq differs from 2cna at 15 residues; 4 Mn++s, 4 Ca++s, and 4 mannosides #1con 2.0 tetramer in crystal - 1 chain given [237]; 2 Cd++s, 1 Ca++s, and 144 HOHs #2ctv 1.95 dimer or tetramer? - 1 chain given [237]; 1 Mn++, 1 Ca++, and 146 HOHs mu-Conotoxin G/IIIA (Conus geographus l.) (1tcg: 1tcg) {SS rich coil} #1tcg NMR monomer [22]; minimized average structure; 3 Hypdroxyprolines; 1 terminal amide; 3 SSs #1tch NMR monomer [22]; minimized average structure; 3 Hypdroxyprolines; R13A mutant, inactive analog; 1 terminal amide; 3 SSs #1tcj NMR monomer - 10 models given [22]; 3 Hypdroxyprolines; 1 terminal amide; 3 SSs #1tck NMR monomer - 10 models given [22]; 3 Hypdroxyprolines; R13A mutant, inactive analog; 1 terminal amide; 3 SSs omega-Conotoxin GVIA (Conus geographus) (1omc: 1omc) {SS rich anti beta} #1cco NMR monomer - 24 models given [28]; source: synthetic; models 13 - 24 are energy minimized; 3 hydroxyprolines and terminal amide; 3 SSs #1omc NMR monomer - 21 models given [28]; 1 terminal amide; 3 SSs Crambin (Crambe abyssinica) (1crn: 1crn) {SS rich a/b/c doubly wound anti beta ud/ud} #1cbn 0.83 monomer [46]; microheterogeneity at res 22 and res 25; alternate atoms positions in many cases; 1 ethanol; 3 SSs #1ccm NMR monomer - 8 models given [46]; microheterogeneity at res 22 and res 25; 3 SSs #1ccn NMR monomer [46]; microheterogeneity at res 22 and res 25; minimized average structure; 3 SSs #1crn 1.5 monomer [46]; 3 SSs #1cnr 1.05 monomer [46]; PL form; 1 EOH; 3 SSs Creatine Amidinohydrolase (Pseudomonas putida) {domain 1: 2-158: a/b/a doubly wound mixed beta ud/cr} {domain 2: 159-271, 390-402: a/b/c doubly wound anti beta ud/cr} {domain 3: 272-389: a/b open face anti beta ud} #1chm 1.9 dimer? - 2 chains given [401]; 2 CMSs and 394 HOHs Cro Repressor Protein (Phage lambda) (1cro.A: 1cro.A) {a/b open face anti beta cr} #1cro 2.2 CA 4 chains in data set (O,A,B,C) [66]; O-B functional unit #4cro 3.9 CA dimer + dsDNA (a2 + d2) - 12 chains given [66, 17] Beta-B2 Crystallin (Bos taurus) (2bb2: 2bb2.A [4gcr]) {domain 1: -2-84: Greek anti beta} [gcr] {domain 2: 85-181: Greek anti beta} [gcr] #2bb2 2.1 dimer (a2) - 1 chain given [181]; 2 SEOs and 92 HOHs Gamma-B Crystallin (Gamma II) (Bos taurus) (4gcr: 4gcr [2bb2.A]) {domain 1: 1-83: Greek anti beta} [gcr] {domain 2: 84-174: Greek anti beta} [gcr] #4gcr 1.47 monomer [174]; supersedes 1gcr; 230 HOHs #1gcs 2.0 monomer [174]; low temp, 150K; 255 HOHs Crystallin Gamma IVA (Bos taurus) (2gcr: 4gcr [2bb2.A]) {domain 1: 1-82: Greek anti beta} [gcr] {domain 2: 83-174: Greek anti beta} [gcr] #2gcr 2.3 monomer [173]; but packs tightly in vivo under some conditions; 122 HOHs Cucumber Basic Protein (Cucumis sativus) (1cbp: 1cbp) {Greek anti beta + alpha} #1cbp 2.5 CA 1 chain given [96]; 1 Cu ion Cucumber Green Mottle Mosaic Virus (CGMMV, watermelon strain) {up down anti alpha + anti beta + coil} #1cgm 3.4 multimer + RNA - 2 chains given [161, 3]; nucleotides modeled as GAA; 5 HOHs Cutinase (Fusarius solani, supsp. pisi) {a/b/a doubly wound para beta ud/ud + coil} #1cus 1.25 monomer? [200]; 216 HOHs; 2 SSs Cyclic-AMP Dependent Protein Kinase, Type I (Bos primigenius taurus) (1apk: 1apk [2apk] [3gap.A]) {domain 1: double stranded beta cylinder + wedge alpha + alpha} {domain 2: double stranded beta cylinder + wedge alpha + alpha} Whole monomer is 379 aa's, each file is 1 of three domains. #1apk --- 1 chain given [379]; model of Type I - Domain A; 1 c-AMP #1bpk --- 1 chain given [379]; model of Type I - Domain B; 1 c-AMP Cyclic-AMP Dependent Protein Kinase, Type II (Bos primigenius taurus) (2apk: 2apk [1apk] [3gap.A]) {domain 1: double stranded beta cylinder + wedge alpha + alpha} {domain 2: double stranded beta cylinder + wedge alpha + alpha} Whole monomer is 400 aa's, each file is 1 of three domains. #2apk --- 1 chain given [400]; model of Type II - Domain A; 1 c-AMP #2bpk --- 1 chain given [400]; model of Type II - Domain B; 1 c-AMP Cyclic-AMP Dependent Protein Kinase, Alpha Isoenzyme (Mus musculus) (1atp.E: 1atp.E) {domain 1: 15-122,317-350: c/b open face anti beta cr + wedge alpha + alpha} {domain 2: 123-316: up down anti alpha + crossed alpha + anti beta} #1apm 2.0 catalytic subunit + inhibitor [350, 20]; S139A mutant; 3 residues are phosphorylated; 1 n-octane and 207 HOHs #1atp 2.2 catalytic subunit + inhibitor [350, 20]; 2 residues are phosphorylated; ATP, 2 Mn++s, and 103 HOHs #2cpk 2.7 catalytic subunit + inhibitor [350, 20]; supersedes 1cpk; 3 residues are phosphorylated Cyclic-AMP Dependent Protein Kinase (Sus scrofa) (1ctp.E: 1atp.E) {domain 1: 7-34,123-324: up down anti alpha + crossed alpha + anti beta} {domain 2: 35-122,325-350: open face anti beta + wedge alpha + alpha} #1ctp 2.9 catalytic subunit + inhibitor [350, 20]; 1 myristate, 1 phos- phoryl group, 2 Is, and 2 HOHs Cyclodextrin Glycosyltransferase (Bacillus circulans, strain 8) (1cgt: 1cgt [6taa]) {domain 1: 1-396: a/b singly wound para beta + anti betas} {domain 2: 397-494: double stranded beta cylinder} {domain 3: 495-581: Greek anti beta} {domain 4: 582-684: Greek anti beta} #1cgt 2.0 monomer? [684]; 2 Ca++s and 588 HOHs; 1 SS #1cgu 2.5 monomer? [684]; D229A mutant; 2 Ca++s, 2 GLCs, and 478 HOHs; 1 SS Cyclodextrin Glycosyltransferase (Bacillus circulans, strain 251) (1cdg: 1cgt [6taa]) {domain 1: 1-406: a/b singly wound para beta} {domain 2: 407-495: double stranded beta cylinder} {domain 3: 496-583: Greek anti beta} {domain 4: 584-686: Greek anti beta} #1cdg 2.0 monomer? [686]; 3 maltoses, 2 Ca++s, and 471 HOHs; 1 SS Cyclophilin (Escherichia coli) {Greek anti beta + alpha caps + coil} #1clh NMR monomer? - 12 models given [166] Cyclophilin (Homo sapiens) (2cpl: 2cpl) {Greek anti beta + alpha caps + coil} #2cpl 1.63 monomer? [164]; 119 HOHs Cyclophilin A (Homo sapiens) {Greek anti beta + alpha caps + coil} #1csa NMR monomer - 18 models given [11]; non-standard amino acids; as bound to cyclophilin, but cyclosporin only; 1 BMT, 1 ABA, 1 SAR, 4 MLEs, and 1 MVA #1cyh 1.64 monomer? + dipeptide - 2 chains given [164, 2]; 80 HOHs #3cys NMR monomer? + cyclosporin - 22 models of 2 chains given [165, 11]; 1 BMT, 1 ABA, 1 SAR, 4 MLEs, and 1 MVA Cyclosporin A (Beauveria nivea) (1cya: ***) {coil: connected ring} #1cya NMR monomer [11]; minimized average structure; non-standard amino acids: 1 3-hydroxy-4-methyl-2-(methylamino)-6-octenoic acid, 1 ABA, 1 sarcosine, 5 N-methylleucines, 1 N-methylvaline, and 1 D-alanine #1cyb NMR monomer - 20 models given [11]; non-standard amino acids: 1 3- hydroxy-4-methyl-2-(methylamino)-6-octenoic acid, 1 ABA, 1 sarco- sine, 5 N-methylleucines, 1 N-methylvaline, and 1 D-alanine Cyclosporin A (Tolypocladium inflatum) (3cys: ***) {coil: connected ring} DUP3cys NMR monomer? + cyclophilin A - 22 models of 2 chains given [165, 11]; 1 BMT, 1 ABA, 1 SAR, 4 MLEs, and 1 MVA Cystatin (Gallus gallus) (1cew.I: 1cew.I) {a/b open face anti beta cr + alpha} see 1stf #1cew 2.0 monomer? [108]; 123 HOHs; 2 SSs Cystatin B (Homo sapiens) (1stf.I: 1stf.I) {a/b open face anti beta cr} see 1cew DUP1stf 2.37 monomer + papain proteinase (i + a) - 2 chains given [98, 212]; C:I8S mutant; 1 carboxymethyl group and 142 HOHs; 3 SSs Cytochrome B5 (Bos taurus) membrane binding tail removed (3b5c: 3b5c [1fcb.A.1]) {heme binding up down anti alpha + a/b open face anti beta ud} [cytb; b5c] #3b5c 1.5 monomer [93]; oxidized; supersedes 2b5c; 1 HEM with Fe+++ and 91 HOHs #1cyo 1.5 monomer [93]; oxidized; 1 HEM with Fe+++ and 117 HOHs Cytochrome B562 (Escherichia coli) (256b.A: 256b.A) {heme up down anti alpha} [256b] #256b 1.4 monomer - 2 chains given [106]; oxidized; supersedes 156b; 2 HEMs with Fe+++, 4 SO4s, and 165 HOHs #1apc NMR monomer [106]; apo form Cytochrome C (Equus caballus) (2pcb.B: 1ycc [1c2r.A] [3c2c]) {crossed alpha + anti beta + heme binding coil} [cytc+] DUP2pcb 2.8 monomer + monomers (2) - 3 chains given [104, 294]; with cyto- chrome C peroxidase; 1 HEM with Fe+++ and 337 HOHs 1frc NMR monomer [104]; minimized average structure; 1 HEM with Fe++ and 6 HOHs Cytochrome C (Katsuwonis pelamis, linnaeus) (1cyc: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc] #1cyc 2.3 monomer [103]; ferro; 1 HEM with Fe++ and 1 HOH Cytochrome C (Thunnus alalunga) (5cyt.R: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc] #3cyt 1.8 dimer (a2) - 2 chains given [103]; oxidized; supersedes 1cyt; 2 HEMs with Fe+++ and 51 HOHs #5cyt 1.5 monomer [104]; reduced; supersedes 4cyt; 1 HEM with Fe++ and 91 HOHs Cytochrome C (Oryza sativa l.) (1ccr: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc] #1ccr 1.5 monomer [112]; 6 methyl groups for 2 trimethyllysine residues, 1 HEM with Fe+++ and 46 HOHs Cytochrome C - Isozyme 1 (Saccharomyces cerevisiae) (1ycc: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc+] XXX Thornton cytochrome #1crg 2.0 monomer [108]; oxidized; N52I and C102T mutant; 1 trimethyl of lysine, 1 HEM with Fe++, 1 SO4, and 45 HOHs #1crh 1.9 monomer [108]; reduced; N52I mutant; 1 trimethyl of lysine, 1 HEM with Fe++, 1 SO4, and 58 HOHs #1cri 2.0 monomer [108]; oxidized; N52I, Y67F, and C102T mutant; 1 tri- methyl of lysine, 1 HEM with Fe++, 1 SO4, and 39 HOHs #1crj 2.05 monomer [108]; reduced; N52I, Y67F, and C102T mutant; 1 trimethyl of lysine, 1 HEM with Fe++, 1 SO4, and 52 HOHs #1cty 2.2 monomer [107]; oxidized; Y67F and C102T mutant; 1 HEM with Fe+++, 1 methyl part of eps-N-trimethyllysine, 1 SO4, and 30 HOHs #1ctz 1.9 monomer [107]; reduced; Y67F and C102T mutant; 1 HEM with Fe+++, 1 methyl part of eps-N-trimethyllysine, 1 SO4, and 48 HOHs #1rap 2.25 monomer [108]; V20F, E21D, K22Q, P25A, and H26N mutant; reduced; 1 trimethyl group on K72, 1 HEM with Fe++, 1 SO4, and 51 HOHs #1raq 1.9 monomer [108]; E21D, K22Q, P25A, and H26N mutant; reduced; 1 tri- methyl group on K72, 1 HEM with Fe++, 1 SO4, and 74 HOHs DUP2pcc 2.3 monomer + monomer - 4 chains given [108, 296]; with cytochrome C peroxidase; 4 HEM with Fe+++, 2 SO4s, and 503 HOHs #1ycc 1.23 monomer [107]; reduced; 3 methyl groups for 1 trimethyllysine, 1 HEM with Fe++, 1 SO4, and 116 HOHs #2ycc 1.9 monomer [107]; oxidized; C102T mutant; 3 methyl groups for 1 tri- methyllysine, 1 HEM with Fe+++, 1 SO4, and 61 HOHs Cytochrome C - Isozyme 2 (Saccharomyces cerevisiae) (1yea: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc+] #1yea 1.9 monomer [112]; reduced; 3 methyl groups for 1 trimethyllysine, 1 HEM with Fe++, 1 SO4, and 58 HOHs Cytochrome C - Composite B-2036 (Saccharomyces cerevisiae) (1yeb: 1ycc [3c2c] [1c2r.A]) {crossed alpha + anti beta + heme binding coil} [cytc+] #1yeb 1.95 monomer [108]; reduced; 3 methyl groups for 1 trimethyllysine, 1 HEM with Fe++, 1 SO4, and 55 HOHs Cytochrome C Peroxidase (Saccharomyces cerevisiae) (2cyp: 2cyp) {domain 1: 2-144,273-297: crossed alpha + anti beta} {domain 2: 145-272: crossed alpha + open face anti beta} [cyp] #1cca 1.8 monomer? [297]; 1 HEM with Fe++ and 49 HOHs #1ccb 2.1 monomer? [297]; D235E mutant; 1 HEM with Fe++ and 50 HOHs #1ccc 2.0 monomer? [297]; D235A mutant; 1 HEM with Fe++ and 51 HOHs #1cce 2.3 monomer? [291]; H175G mutant; 1 HEM with Fe++ and 86 HOHs #1ccg 2.1 monomer? [291]; H175G mutant; 1 HEM with Fe++, 1 IMD, and 84 HOHs #1ccp 2.2 monomer [296]; native + two N-terminal aa's from expression in E.coli; sequence differs from 2cyp at 2 aa's -- strain- related; 1 HEM with Fe+++ and 234 HOHs #2ccp 2.2 monomer [296]; D235N mutant; 1 HEM with Fe+++ and 245 HOHs #3ccp 2.2 monomer [296]; W191F mutant; 1 HEM with Fe+++ and 199 HOHs #4ccp 2.2 monomer [296]; W51F mutant; 1 HEM with Fe+++ and 212 HOHs #5ccp 2.2 monomer [296]; Ins(MI), H52L mutant; 1 HEM with Fe+++ and 197 HOHs #6ccp 2.2 monomer [296]; R48K mutant; 1 HEM with Fe+++ and 198 HOHs #7ccp 2.2 monomer [296]; Ins(MI), R48L mutant; 1 HEM with Fe+++ and 210 HOHs #1cmp 1.9 monomer [294]; variant strain + W191G mutant; 2 norleucines, 1 HEM with Fe++, 1 2,3-dimethylimidazolium ion, and 50 HOHs #1cmq 2.3 monomer [294]; variant strain + W191G mutant; 2 norleucines, 1 HEM with Fe++, and 55 HOHs #1cpd 2.2 monomer [296]; Ins(MI), W191G mutant; 1 HEM with Fe+++, 1 NH4, and 216 HOHs #1cpe 2.2 monomer [296]; Ins(MI), W191G mutant; 1 HEM with Fe+++, 1 K+, and 210 HOHs #1cpf 2.2 monomer [296]; Ins(MI), W191G mutant; 1 HEM with Fe+++, 1 TRS, and 197 HOHs #1cpg 2.2 monomer [296]; Ins(MI), W191Q mutant; 1 HEM with Fe+++, 1 K+, and 197 HOHs #2cyp 1.7 monomer [294]; 1 HEM with Fe+++ and 262 HOHs #1dcc 2.2 monomer [296]; Ins(MI), W191F mutant; 1 O2, 1 HEM with Fe++, and 182 HOHs #2pcb 2.8 monomers (2a) + monomer - 3 chains given [296, 104]; with cyto- chrome C (horse); 3 HEMs with Fe+++ and 337 HOHs #2pcc 2.3 monomer + monomer - 4 chains given [296, 108]; with cyto- chrome C (yeast); 4 HEMs with Fe+++, 2 SO4s, and 503 HOHs Cytochrome C Prime (Chromatium vinosum) (1bbh.A: 1bbh.A) {heme binding up down anti alpha + anti beta cap} #1bbh 1.8 dimer (a2) - 2 chains given [131]; 2 HEMs with Fe++ and 221 HOHs Cytochrome C Prime (Rhodospirillum molischianum) (2ccy.A: 2ccy.A) {heme binding up down anti alpha + anti beta cap} [256b] #2ccy 1.67 dimer (a2) - 2 chains given [128]; 2 HEMs with Fe+++ and 194 HOHs Cytochrome C2 (formerly Cytochrome C550) (Paracoccus denitrificans) (155c: 1c2r.A [3c2c] [1ycc]) {crossed alpha + heme binding coil} [cytc] or {domain 1: 2-43,105-122: up down alpha-coils + coil} XXX {domain 2: 44-104: a/b open face anti beta ud} #155c 2.5 monomer [135]; some UNK residues at C terminus; 1 HEM with Fe++ #1cot 1.7 monomer [129]; 1 HEM with Fe++ and 103 HOHs Cytochrome C2 (Rhodobacter capsulatus) (1c2r.A: 1c2r.A [1ycc] [3c2c]) {crossed alpha + anti betas + heme binding coil} [cytc+] #1c2r 2.5 monomer - 2 chains given [116]; oxidized; 2 HEMs with Fe++ and 92 HOHs Cytochrome C2 (Rhodopseudomonas viridis) {crossed alphas + heme binding coil} #1cry 3.0 monomer [107]; HEM with Fe++ Cytochrome C2 (Rhodospirillum rubrum) (3c2c: 3c2c [1c2r.A] [1ycc]) {crossed alpha + anti betas + heme binding coil} [cytc] #2c2c 2.0 monomer [112]; oxidized; supersedes 1c2c; 1 HEM with Fe+++ and 87 HOHs #3c2c 1.68 monomer [112]; reduced; 1 HEM with Fe++ and 87 HOHs Cytochrome C3 (Desulfovibrio desulfuricans Hildenborough) (1cth.A: 2cdv [2cy3]) {heme binding anti alpha + anti beta + coil} [cytc3+] #1cth 1.9 monomer - 2 chains given [107]; 8 HEMs with Fe and 83 HOHs Cytochrome C3 (Desulfovibrio desulfuricans Norway) (2cy3: 2cy3 [2cdv]) {heme binding anti alpha + anti beta + coil} [cytc3] #2cy3 1.7 monomer [118]; 4 HEMs with Fe; supersedes 1cy3 Cytochrome C3 (Desulfovibrio vulgaris miyazaki iam 12604) (2cdv: 2cdv [2cy3]) {heme binding anti alpha + anti beta + coil} [cytc3] #2cdv 1.8 monomer [107]; supersedes 1cdv; 4 HEMs with Fe and 47 HOHs Cytochrome C5 (Azotobacter vinelandii) (1cc5: 1cc5) {heme binding crossed alpha + anti beta + coil} [cc5] XXX Thornton cytochrome #1cc5 2.5 monomer [83]; 1 HEM with Fe+++; 1 SS Cytochrome C551 (Pseudomonas aeruginosa) (351c: 351c) {crossed alpha + anti betas + heme binding coil} [cytc] XXX Thornton cytochrome #351c 1.6 monomer [82]; oxidized; supersedes 251c; 1 HEM with Fe+++ with reduced vinyl groups and 67 HOHs #451c 1.6 monomer [82]; reduced; 1 HEM with Fe++ with reduced vinyl groups and 73 HOHs #2pac NMR monomer - 10 models given [82]; 1 HEM with Fe++ Cytochrome C551 (Pseudomonas stutzeri) (1cor: 351c) {crossed alpha + anti betas + heme binding coil} [cytc+] #1cch NMR monomer - 1 model given [82]; minimized average structure; 1 HEM with Fe++ #1cor NMR monomer - 1 model given [82]; minimized average structure; 1 HEM with Fe++ Cytochrome C551I (unknown) (2mta.C: 2mta.C) {crossed alpha + anti betas + heme binding coil} [cytc+] DUP2mta 2.4 monomer + methylamine dehydrogenase + amicyanin (2c + a2b2 + 2d) - 4 chains given [147, 373, 125, 105]; cytochrome is not fit to electron density -- simulated from another cytochrome C551; 2 Os bound to indole ring of L:W57, 1 Cu++, 1 HEM with Fe++, 1 phosphate, and 127 HOHs; 7 SSs Cytochrome C553 (Desulfovibrio vulgaris miyazaki F) (1c53: 1c53) {crossed alpha + heme binding coil} [cytc+] #1c53 1.8 CA monomer [79]; 1 HEM with Fe++ and reduced vinyl groups Cytochrome F (Brassica rapa) {domain 1: 1-166,231-250: a/b/b/a+c back to back open face anti betas ud/cr} {domain 2: 167-230: Greek anti beta} #1ctm 2.3 monomer? [250]; 1 HEM with Fe++ and 113 HOHs Cytochrome P450 BM3 (Bacillus megaterium) (2hpd.A: 2hpd.A) {domain 1: 1-72,330-371: a/b open face anti beta ud + anti beta + open face anti beta + wedge alpha} {domain 2: 73-329,372-472: Greek anti alpha + anti beta} XXX [cpp+] #2hpd 2.0 monomer? - 2 chains given [471]; hemoprotein domain; 2 HEMs with Fe+++s and Os and 453 HOHs Cytochrome P450CAM (Camphor Monooxygenase) (Pseudomonas putida) (2cpp: 2cpp [1scc] [1cpt]) {domain 1: 10-96,298-331: a/b open face anti beta cr + anti beta + open face anti beta + alpha} {domain 2: 97-297,332-414: Greek anti alpha + anti beta} XXX [cpp] #1cp4 1.9 monomer [414]; 1 HEM with Fe+++, 1 benzene, and 203 HOHs #2cp4 2.1 monomer [414]; T252A mutant; 1 HEM with Fe+++, 1 camphor, and 232 HOHs #3cp4 2.3 monomer [414]; 1 HEM with Fe+++, 1 adamantane, and 204 HOHs #4cp4 2.1 monomer [414]; 1 HEM with Fe+++, 1 camphor, and 204 HOHs #2cpp 1.63 monomer [414]; supersedes 1cpp; 1 HEM with Fe+++, 1 camphor, and 204 HOHs #3cpp 1.9 monomer [414]; 1 HEM with Fe+++ and CO, 1 reduced camphor, and 238 HOHs #4cpp 2.11 monomer [414]; 1 HEM with Fe+++, 1 adamantane, and 202 HOHs #5cpp 2.08 monomer [414]; 1 HEM with Fe+++, 1 adamantanone, and 204 HOHs #6cpp 1.9 monomer [414]; 1 HEM with Fe+++, 1 camphane, and 204 HOHs #7cpp 2.0 monomer [414]; 1 HEM with Fe+++, 1 norcamphor, and 206 HOHs #8cpp 2.1 monomer [414]; 1 HEM with Fe+++, 1 thiocamphor, and 205 HOHs #1pha 1.63 monomer [414]; camphor, plus isomer; 1 HEM with Fe++, 1 1-(N-im- idazolyl)-2-hydroxy-2-(2,3-dichlorophenyl)octane, and 205 HOHs #1phb 1.6 monomer [414]; camphor, minus isomer; 1 HEM with Fe++, 1 1-(N- imidazolyl)-2-hydroxy-2-(2,3-dichlorophenyl)octane, and 213 HOHs #1phc 1.6 monomer [414]; 1 HEM with Fe++ and 192 HOHs #1phd 1.6 monomer [414]; 1 HEM with Fe++, 2-phenyl imidazole, and 204 HOHs #1phe 1.6 monomer [414]; 1 HEM with Fe++, 2-phenyl imidazole, 1 SO4, and 205 HOHs #1phf 1.6 monomer [414]; 1 HEM with Fe++, 4-phenyl imidazole, and 206 HOHs #1phg 1.6 monomer [414]; 1 HEM with Fe, 1 metyrapone, and 204 HOHs Cytochrome P450SCC (Pseudomonas putida) (1scc: 1scc [1cpt] [2cpp]) {domain 1: 1-98,350-389: anti betas + anti alphas + coil} {domain 2: 99-349,390-482: Greek anti alpha + anti beta} XXX [cpp+] #1scc --- monomer [481]; non-experimental model, no heme Cytochrome P450TERP (Pseudomonas sp.) (1cpt: 1cpt [1scc] [2cpp]) {domain 1: 1-98,316-355: a/b open face anti beta cr + anti beta + open face anti beta + alpha} {domain 2: 99-315,356-428: Greek anti alpha + anti beta} XXX [cpp+] #1cpt 2.3 monomer [412]; 1 HEM with Fe++ and 221 HOHs Cytotoxic T-Lymphocyte Proteinase I (Mus musculus) (2cp1: 2cp1 [2cga.A] [3est] [1tgn] [1hf1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: Greek anti beta + alpha} {domain 2: Greek anti beta} [s_prot+] #2cp1 --- 1 chain [227]; non-experimental model Decorsin (Macrobdella decora) {anti betas + coil} #1dec NMR monomer - 25 models given [39]; 3 SSs Defensin HNP-3 (Homo sapiens) (1dfn.A: 1dfn.A) {SS rich open face anti beta} #1dfn 1.9 dimer (a2) - 2 chains given [31]; membrane permeating; 44 HOHs; 6 SSs Delta-Endotoxin CRYIIIA (Bacillus thuringiensis, subs. tenebrionis) {domain 1: 61-300: up down anti alpha} or {domain 1: 61-300: encircled axial alpha} XXX {domain 2: 301-500: Greek anti beta} {domain 3: 501-644: double stranded beta cylinder} #1dlc 2.5 monomer? [584]; 106 HOHs Alpha-Dendrotoxin (Dendroaspis angusticeps) (1dtx: 1dtx [9pti] [1aap.A]) {SS rich a/b open face anti beta ud + coil} #1dtx 2.2 monomer [59]; 5 SO4s and 59 HOHs; 3 SSs Dendrotoxin I (Dendroaspis polylepis polylepis) {SS rich a/b open face anti beta ud + coil} #1dem NMR monomer [60]; minimized average structure; 3 SSs #1den NMR monomer -29 models given [60]; 3 SSs Dendrotoxin K (Dendroaspis polylepis polylepis) (1dtk: 1dtx [9pti] [1aap.A]) {SS rich a/b open face anti beta ud + coil} #1dtk NMR monomer? - 20 models given [57]; 3 SSs Deoxyribonuclease I (Bos taurus) (3dni: 3dni) {back to back a/b open face mixed beta} #1atn 2.8 monomer + actin monomer - 2 chains given [260, 373]; 1:1 indefinitely large multimer; methylated A:H73; 2 NAGs, 1 alpha- D-mannose, 1 ATP, 4 divalent metals, probably Ca++; 2 SSs #3dni 2.0 monomer [260]; 2 NAGs, 5 MANs, 2 Ca++s, and 375 HOHs; 2 SSs #2dnj 2.0 monomer + DNA dimer (ab) [260, 8, 6]; 5'-GCGATCGC-3'; 1 NAG and 252 HOHs; 1 SS #1dnk 2.3 monomer + DNA dimer (a + cd) [260, 8/7]; 5'-GGTATACC-3'; 2 NAGs and 77 HOHs; 1 SS Deoxyribonucleic Acid (DNA) 5'-TG-3' #1dn8 1.5 dimer (a2) - 2 chains given [2]; 1 cobalt hexammine Deoxyribonucleic Acid (DNA) 5'-CG-3' and 5'-CGCG-3' #1d53 1.50 tetramer (a2b2) - 4 chains given [2, 4]; 69 HOHs Deoxyribonucleic Acid (DNA) 5'-CCGG-3' #1ana 2.1 dimer - 2 chains given [4]; A; 5'I-CCGG; 2 iodines and 86 HOHs Deoxyribonucleic Acid (DNA) 5'-CGAC-3' DUP1brn 1.76 monomer + endonulease - 4 chains given [4, 110]; 229 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCG-3' #1zna 1.6 dimer - 2 chains given [4]; Z; high salt; 84 HOHs #1d32 1.7 dimer (a2) - 2 chains given [4]; 1 ditercalinium and 83 HOHs Deoxyribonucleic Acid (DNA) 5'-TTTT-3' DUP1rta 2.5 monomer + ribonuclease - 2 chains given [4, 124]; 4 SSs Deoxyribonucleic Acid (DNA) 5'-ACGCC-3' DUP1hvn NMR ssDNA + Zn finger - 15 models given [5, 17]; with hbond constraints to GUA base; 1 Zn++ DUP1hvo NMR ssDNA + Zn finger - 15 models given [5, 17]; 5'-ACGCC-3'; without hbond constraints to GUA base Deoxyribonucleic Acid (DNA) 5'-CGATCG-3' and variants #1d10 1.5 dimer (a2) - 1 chain given [6]; 1 daunomycin, 1 spermine, 1 Na, and 60 HOHs #1d12 1.7 dimer (a2) - 1 chain given [6]; 1 adriamycin, 1 spermine, 1 Na, and 56 HOHs #1d14 1.5 dimer (a2) - 1 chain given [6]; A 4 is phosphorothioate; 1 S, 1 11-deoxydaunomycin, and 37 HOHs #1d15 1.5 dimer (a2) - 1 chain given [6]; 1 4'-epiadriamycin, 1 spermine, and 38 HOHs #1d37 1.8 dimer (a2) - 1 chain given [6]; 1 4-O-demethyl-11-deoxydoxo- rubicin and 42 HOHs #1d38 1.7 dimer (a2) - 1 chain given [6]; 1 4-demethoxy-daunorubicin, 1 Mg, and 60 HOHs #1da0 1.5 dimer (a2) - 1 chain given [6]; 1 daunomycin Deoxyribonucleic Acid (DNA) 5'-CGCG+CG-3' #1da2 1.7 dimer (a2) - 2 chains given [6]; 2 methoxys and 67 HOHs Deoxyribonucleic Acid (DNA) 5'-CGUACG-3' #1d40 1.3 dimer (a2) - 2 chains given [6]; 5'-M5-CGUA-M5-CG-3'; 3 Cus, 1 CuCl, and 86 HOHs #1d41 1.3 dimer (a2) - 2 chains given [6]; Z; 5'-M5-CGUA-M5-CG-3'; 2 Mgs and 60 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGCG-3' and variants #131d 1.0 dimer (a2) - 2 chains given [6]; 2 spermines, 2 Na+s, and 62 HOHs #133d 1.8 dimer (a2) - 2 chains given [6]; 5'-CGCG+CG-3'; 2 methyls and 49 HOHs #1d24 1.9 dimer (a2) - 2 chains given [6]; 5'-CGC+GCG-3'; O 6 Me on G; 60 HOHs #1d33 1.5 dimer (a2) - 1 chain given [6]; 1 daunorubicin (daunomycin), 1 Mg, and 65 HOHs #1d39 1.2 dimer (a2) - 2 chains given [6]; Z; 6 Cus, 1 Na, and 66 HOHs #1d48 1.0 dimer (a2) - 2 chains given [6]; 1 spermine and 47 HOHs #1dcg 1.0 dimer (a2) - 2 chains given [6]; left-handed; 4 Mgs and 84 HOHs #2dcg 0.9 dimer (a2) - 2 chains given [6]; left-handed; 1 Mg, 2 spermines, and 74 HOHs #1dn4 1.4 dimer (a2) - 2 chains given [6]; left-handed; Cs are brominated; 18 deg C; 6 Brs and 61 HOHs #1dn5 1.4 dimer (a2) - 2 chains given [6]; left-handed; Cs are brominated; 37 deg C; 6 Brs and 81 HOHs #1dnf 1.5 dimer (a2) - 2 chains given [6]; 5'-CGCGUG-3'; 2 Fs, 1 Mg, and 58 HOHs Deoxyribonucleic Acid (DNA) 5'-CGGCCG-3' and variants #110d 1.9 dimer - 1 chain given [6]; 1 daunomycin and 49 HOHs Deoxyribonucleic Acid (DNA) 5'-CGGGCG-3' #145d 1.3 dimer (ab) - 4 chains given [6]; 5'-+CGGG+CG-3' and complement; Z; 8 methyl groups and 48 HOHs Deoxyribonucleic Acid (DNA) 5'-CGTACG-3' and variants #1d11 1.2 dimer (a2) - 1 chain given [6]; 1 daunomycin, 1 Na, and 84 HOHs #1d17 2.0 dimer (a2) - 1 chain given [6]; 5'-M5-CGTA-M5-CG-3'; 1 nogala- mycin and 39 HOHs #1d21 1.7 dimer (a2) - 2 chains given [6]; 5'-M5-CGT-S-A-M5-CG-3'; 2 no- galamycins and 77 HOHs #1d22 1.8 dimer (a2) - 2 chains given [6]; 5'-M5-CGT-S-A-M5-CG-3'; 2 U-58872 derivatives of nogalamycin and 75 HOHs #2d34 1.4 dimer (a2) - 1 chain given [6]; 5'-CGT+ACG-3'; 1 daunorubicin, 1 Mg, and 64 HOHs #1d35 1.3 dimer (a2) - 1 chain given [6]; CGTP==/NH2$==*ACG; 1 daunorubicin derivative MAR70, 1 Mg, and 68 HOHs #1d36 1.5 dimer (a2) - 1 chain given [6]; 1 daunorubicin derivative MAR70, 1 Mg, and 68 HOHs #1d76 1.3 dimer (a2) - 2 chains given [6]; 5'-CGU+ACG-3'; +A is 2-amino- adenine; 84 HOHs #2des 1.5 dimer (a2) - 2 chains given [6]; 2 morpholino-doxorubicins, 1 Mg, 2 Nas, and 79 HOHs Deoxyribonucleic Acid (DNA) 5'-GATATC-3' #2da8 NMR dimer (a2) + peptides (p2) - 4 chains given [6, 5]; 2 2-carboxy- quinoxalines and 2 methyl groups bound to Cys 3; 1 SS Deoxyribonucleic Acid (DNA) 5'-G+CG+CG+C-3' #1d97 2.17 dimer (a2) - 2 chains given [6]; atom O1P of each cytidine re- placed by S; 6 Ss and 72 HOHs Deoxyribonucleic Acid (DNA) 5'-TGATCA-3' #1d58 1.7 dimer (a2) - 1 chain given [6]; 1 4'-epiadriamycin and 34 HOHs #1d67 1.6 dimer (a2) - 1 chain given [6]; 1 4-demethoxy-daunorubicin and 35 HOHs Deoxyribonucleic Acid (DNA) 5'-TGGCCA-3' #1da9 1.7 dimer (a2) - 1 chain given [6]; 1 adriamycin and 43 HOHs Deoxyribonucleic Acid (DNA) 5'-TGTACA-3' #1d54 1.4 dimer (a2) - 1 chain given [6]; 1 4'-epiadriamycin and 33 HOHs Deoxyribonucleic Acid (DNA) 5'-UGCGCG-3' #1da1 2.25 dimer (a2) - 2 chains given [6]; uridines are methylated; 2 Brs, 1 Mg, and 67 HOHs Deoxyribonucleic Acid (DNA) 5'-TTGGGGT-3' #139d NMR tetramer? (a4) - 4 chains given [7]; tetrahymena telomeric G-quadruplex Deoxyribonucleic Acid (DNA) 5'-AAGGCCTT-3' #1d83 NMR dimer (a2) - 2 chains given [8]; 1 chromomycin bound as a Mg++ coordinated dimer Deoxyribonucleic Acid Pribnow Box (DNA) 5'-CATTATAC-3' #1d70 NMR dimer (ab) - 4 models of 2 chains given [8]; last is average structure Deoxyribonucleic Acid (DNA) 5'-CGAGCTCG-3' DUP2rve 3.0 dsDNA + protein dimer (d4 + a2) - 6 chains given [8, 244]; DEL M1; 68 HOHs Deoxyribonucleic Acid (DNA) 5'-CTCTAGAG-3' #1d93 2.15 dimer (a2) - 1 chain given [8]; 35 HOHs Deoxyribonucleic Acid (DNA) 5'-GAAGCTTC-3' #1d55 3.0 dimer + peptides (a2 + b2) - 4 chains given [8, 5]; 2 sarcosyl groups, 2 methyl groups, 1 2-amino-1,9-dicarboxy-4,6 dimethyl-3- phenoxazone, and 107 HOHs Deoxyribonucleic Acid (DNA) 5'-GCCCGGGC-3' #9dna 1.8 dimer (a2) - 1 chain given [8]; 34 HOHs #1d26 2.12 dimer (a2) - 1 chain given [8]; 5'-GCCC+GGGC-3'; methylene phos- phonate on +G; 29 HOHs Deoxyribonucleic Acid (DNA) 5'-GCGATCGC-3' DUP2dnj 2.0 dimer (ab) + nuclease - 3 chains given [8, 6, 260]; 1 NAG and 252 HOHs; 1 SS Deoxyribonucleic Acid (DNA) 5'-GGGCGCCC-3' #2d94 1.7 dimer (a2) - 1 chain given [8]; tetragonal, 293K; 44 HOHs #2d95 2.0 dimer (a2) - 1 chain given [8]; tetragonal, 115K; 40 HOHs Deoxyribonucleic Acid (DNA) 5'-GGGGCCCC-3' #2ana 2.5 dimer - 2 chains given [8]; A Deoxyribonucleic Acid (DNA) 5'-GGGATCCC-3' #3ana 2.5 dimer - 2 chains given [8]; A; 9 HOHs Deoxyribonucleic Acid (DNA) 5'-GGGGTCCC-3' #1d91 2.1 dimer (a2) - 2 chains given [8]; 104 HOHs Deoxyribonucleic Acid (DNA) 5'-GGGGCTCC-3' #1d92 2.25 dimer (a2) - 2 chains given [8]; 52 HOHs Deoxyribonucleic Acid (DNA) 5'-GGIGCTCC-3' #1d90 1.7 dimer (a2) - 2 chains given [8]; 81 HOHs Deoxyribonucleic Acid (DNA) 5'-GGTATACC-3' DUP1dnk 2.3 dimer (ab) + monomer (ab + p) [8/7, 260]; 2 NAGs and 77 HOHs Deoxyribonucleic Acid (DNA) 5'-GG+UA+UACC-3' #115d 1.7 dimer - 2 chains given [8]; 4 Brs and 85 HOHs Deoxyribonucleic Acid (DNA) 5'-GTACGTAC-3' and reverse #28dn 2.4 dimer (a2) - 1 chain given [8]; 56 HOHs #5ana 2.25 dimer (a2) - 1 chain given [8]; 1 Mg++ and 52 HOHs #1d18 NMR dimer (a2) - 1 model of 2 chains given [8]; 5'-CATGCATG-3'; reverse of 1d19 #1d19 NMR dimer (a2) - 1 model of 2 chains given [8]; reverse of 1d18 Deoxyribonucleic Acid (DNA) 5'-GTATATAC-3' #1d42 NMR dimer (a2) - 2 chains given [8] Deoxyribonucleic Acid (DNA) 5'-GTCACATG-3' #124d NMR dimer (ab) - 2 chains given [8] Deoxyribonucleic Acid (DNA) 5'-GTCTAGAC-3' #1d82 2.5 dimer (a2) - 1 chain given [8]; 3 HOHs Deoxyribonucleic Acid (DNA) 5'-GTGTACAC-3' #1dns 2.0 dimer (a2) - 1 chain given [8]; 1 spermine (one half molecule) #1d78 1.4 dimer (a2) - 1 chain given [8]; 37 HOHs #1d79 1.45 dimer (a2) - 1 chain given [8]; 35 HOHs Deoxyribonucleic Acid (DNA) 5'-AGACGTCTA-3' + 5'-TTAGACGTCT-3' DUP1cma 2.8 dimer + repressor (d2 + a2) - 4 chains given [9, 10, 104]; 2 S-adenosylmethionine and 36 HOHs Deoxyribonucleic Acid (DNA) 5'-CTCCCATCC-3' #1dn6 3.0 dimer (ab) - 2 chains given [9]; non-standard complement Deoxyribonucleic Acid (DNA) 5'-ACCGGCCGGT-3' #1d13 2.0 dimer (a2) - 1 chain given [10]; 36 HOHs Deoxyribonucleic Acid (DNA) 5'-CATGGCCATG-3' #126d 2.0 dimer (a2) - 2 chains given [10]; 49 HOHs Deoxyribonucleic Acid (DNA) 5'-CCAACITTGG-3' #1d60 2.2 dimer (a2) - 2 chains given [10]; 1 Mg with 6 HOHs and 36 HOHs #1d61 1.3 dimer (a2) - 2 chains given [10]; 1 cacodylate, 1 Ca with 7 HOHs and 72 HOHs Deoxyribonucleic Acid (DNA) 5'-CCAAIATTGG-3' #1d62 2.0 dimer (a2) - 1 chain given [10]; 50 HOHs Deoxyribonucleic Acid (DNA) 5'-CCAAGATTGG-3' #3dnb 1.3 dimer - 2 chains given [10]; 5'-CCAAGATTGG-3'; 3 Mg and 69 HOHs Deoxyribonucleic Acid (DNA) 5'-CCAxxxxTGG-3' #122d 1.7 dimer - 2 chains given [10]; 5'-CCAGGC+CTGG-3'; refined using TNT; 2 methyl groups on cytidines and 37 HOHs #123d 1.7 dimer - 2 chains given [10]; 5'-CCAGGC+CTGG-3'; methylated derivative of 1bd1; refined using XPLOR; 2 methyl groups on cytidines and 80 HOHs #1bd1 1.6 dimer - 1 chain given [10]; B; 5'-CCAGGCCTGG-3'; 2 triethyl- ammonium+s and 41 HOHs #2d25 1.75 dimer (a2) - 2 chains given [10]; 5'-CCAGGC+CTGG-3'; +C is methylated; refined using NUCLSQ; 80 HOHs #5dnb 1.4 dimer - 1 chain given [10]; 5'-CCAACGTTGG-3'; 4 Mgs and 77 HOHs Deoxyribonucleic Acid (DNA) 5'-CCGGCGCCGG-3' #1cgc 2.20 dimer (a2) - 2 chains given [10]; 47 HOHs Deoxyribonucleic Acid (DNA) 5'-CGATCCATCG-3' #1d23 1.5 dimer (a2) - 2 chains given [10]; 2 hydrated Mgs and 142 HOHs Deoxyribonucleic Acid (DNA) 5'-CGATCG+ATCG-3' #1da3 2.0 dimer (a2) - 2 chains given [10]; 2 methyl groups, 1 Cl-, 2 hydrated Mg++s, and 45 HOHs Deoxyribonucleic Acid (DNA) 5'-CGATTAATCG-3' #1d49 1.5 dimer (a2) - 2 chains given [10]; 1 Mg and 108 HOHs Deoxyribonucleic Acid (DNA) 5'-CGATATATCG-3' #1d56 1.70 dimer (a2) - 2 chains given [10]; 1 Ca++ with 7 HOHs coordi- nated and 87 HOHs #1d57 2.00 dimer (a2) - 2 chains given [10]; 1 Mg++ with 6 HOHs coordi- nated and 55 HOHs Deoxyribonucleic Acid (DNA) 5'-CGGTGATAGA-3' #1d20 NMR dimer (ab) - 2 chains given [10] Deoxyribonucleic Acid (DNA) 5'-GCGGGCCCGC-3' #137d 1.7 dimer - 2 chains given [10]; orthorhombic crystal form;101 HOHs #138d 1.8 dimer - 1 chain given [10]; hexagonal crystal form; 38 HOHs Deoxyribonucleic Acid (DNA) 5'-GCGTATACGC-3' #1d68 NMR dimer (a2) - 2 chains given [10] #1d87 2.25 dimer (a2) - 2 chains given [10]; 110 HOHs #1d88 2.00 dimer (a2) - 2 chains given [10]; 110 HOHs Deoxyribonucleic Acid + Ribonucleic Acid Hybrid (DNA/RNA) 5'-R(GCG)- D(TATACGC)- 3' #1d96 2.0 dimer (a2) - 2 chains given [10] Deoxyribonucleic Acid + Ribonucleic Acid - Okazaki Fragment (DNA + RNA) #1ofx 2.00 dimer - 2 chains given [10]; 5'-GGGTATACGC-3' + 5'-R(GCG)- D(TATACCC)-3'; 1 spermine and 93 HOHs Deoxyribonucleic Acid (DNA) 5'-GGGATATCCC-3' DUP4rve 3.0 dsDNA + protein dimer (d4 + a2) - 6 chains given [10, 244]; DEL M1; 23 HOHs LAC Operator (Escherichia coli, Strain BMH 74-12) 5'-AATTGTGAGCG-3' DUP1lcc NMR dsDNA + repressor (cd + a) - 3 chains given [11, 11, 51]; left half of operator; minimized average structure; 1 Na+ and 53 HOHs DUP1lcd NMR dsDNA + repressor (cd + a) - 3 models of 3 chains given [11, 11, 51]; left half of operator; 1 Na+ and 53 HOHs Deoxyribonucleic Acid ZIF268 Gene (Homo sapiens) 5'-AGCGTGGGCGT-3' DUP1zaa 2.1 dsDNA + monomer - 3 chains given [11, 85]; 3 Zn++s and 129 HOHs Deoxyribonucleic Acid (DNA) 5'-ATGAGCGAATA-3' #1d69 NMR dimer (a2) - 2 chains given [11] Deoxyribonucleic Acid (DNA) 5'-CCACCCCAAAC-3' DUP2dpv 3.25 DNA + virus capsid (a60) - 2 chains given [584, 11]; 2 divalent metal ions; 1 SS Deoxyribonucleic Acid (DNA) 5'-CCCCCGCGGGGG-3' #2d47 2.0 dimer (a2) - 2 chains given [12]; 1 spermine and 107 HOHs Deoxyribonucleic Acid (DNA) 5'-CCGTACGTACGG-3' and 5'-GCGTACGTACGC-3' #116d 2.5 dimer - 1 chain given [12]; A?; 5'-CCGTACGTACGG-3'; 40 HOHs #117d 2.5 dimer - 1 chain given [12]; A; 5'-GCGTACGTACGC-3'; 33 HOHs Deoxyribonucleic Acid (DNA) 5'-CGAGAATTCGCG-3' #153d 2.9 dimer (a2) - 2 chains given; 5'-CGAGAATTC+GCG-3'; 2 methyls bonded to O6 and 49 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCAAATTTGCG-3' and variants #111d 2.25 dimer (a2) - 2 chains given [12]; 5'-CGCAAATTGGCG-3'; 62 HOHs #121d 2.2 dimer (a2) - 2 chains given [12]; 1 netropsin and 47 HOHs #1d63 2.00 dimer (a2) - 2 chains given [12]; 1 berenil, 1 Mg++, and 65 HOHs #1d65 2.20 dimer (a2) - 2 chains given [12]; 71 HOHs #1d81 2.5 dimer (a2) - 2 chains given [12]; 5'-CGCAAATTIGCG-3'; 71 HOHs #2dnd 2.2 dimer (a2) - 2 chains given [12]; 1 distamycin and 75 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCAAAAATGCG-3' #1bdn 2.6 dimer (ab) - 4 chains given [12]; B; 2 Mg++s and 21 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCAAAAAAGCG-3' #1d98 2.5 dimer (ab) - 2 chains given [12]; 21 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCATATATGCG-3' #1dn9 2.2 dimer (a2) - 2 chains given [12]; 5'-CGCATATATGCG-3'; 43 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGAAAAAACG-3' #1d89 2.3 dimer (ab) - 6 chains given [12]; 55 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGAAAACGCG-3' #1ndn 3.0 trimer - 6 chains given [12, 6, 6]; 5'-CGCGAAAACGCG-3'; short chains are complementary to long chain; 133 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCAAATTCGCG-3' #1d99 2.5 dimer (a2) - 2 chains given [12]; 78 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGAATTCGCG-3' and variants #112d 2.5 dimer (a2) - 2 chains given [12]; B; 5'-CGCGAATTAGCG-3'; 83 HOHs #113d 2.5 dimer (a2) - 2 chains given [12]; B; 5'-CGCGAATTTGCG-3'; 72 HOHs #114d 2.5 dimer (a2) - 2 chains given [12]; B; 5'-CGCIAATTAGCG-3'; 64 HOHs #127d 2.0 dimer (a2) - 2 chains given [12]; 1 Hoechst 33258 and 121 HOHs #128d 2.5 dimer (a2) - 2 chains given [12]; 5'-CGC+GAATTCGCG-3'; 2 ethyl groups bonded to O6 of +G, 1 Hoechst 33258, and 68 HOHs #129d 2.25 dimer (a2) - 2 chains given [12]; 1 Hoechst 33342 and 64 HOHs #130d 2.5 dimer (a2) - 2 chains given [12]; 5'-CGC+GAATTCGCG-3'; 2 ethyl groups bonded to O6 of +G, 1 Hoechst 33342, and 68 HOHs #1bna 2.3 dimer (a2) - 2 chains given [12]; B; 290K; 80 HOHs #2bna 2.7 dimer (a2) - 2 chains given [12]; B; 16K; 83 HOHs #3bna 3.0 dimer (a2) - 2 chains given [12]; B; 5'-CGCGAATT-Br-CGCG-3'; 298K; 60% MPD; 2 Brs and 44 HOHs #4bna 2.3 dimer (a2) - 2 chains given [12]; B; 5'-CGCGAATT-Br-CGCG-3'; 277K; 60% MPD; 2 Brs and 114 HOHs #5bna 2.6 dimer (a2) - 2 chains given [12]; B; complex with cisplatin; 128 HOHs #6bna 2.21 dimer (a2) - 2 chains given [12]; B; 5'-CGCGAATT-Br-CGCG-3'; 2 Brs, 1 netropsin, and 75 HOHs #7bna 1.9 dimer (a2) - 2 chains given [12]; B; 290K; 78 HOHs; includes anisotropy factors #8bna 2.2 dimer (a2) - 2 chains given [12]; B; 1 Hoechst 33258, 1 Mg, and 175 HOHs #9bna 1.9 dimer (a2) - 2 chains given [12]; B; 64 HOHs #1d27 2.0 dimer (a2) - 2 chains given [12]; 5'-CGC+GAATTTGCG-3'; +G is O6- methylguanine; 69 HOHs #1d31 2.6 dimer (a2) - 2 chains given [13]; 5'-CGCAGAATTCGCG-3'; has bulge #1d43 2.0 dimer (a2) - 2 chains given [12]; 0 deg C; piperazine up; 1 Hoecsht 33258, 1 Mg, and 61 HOHs #1d44 2.0 dimer (a2) - 2 chains given [12]; 0 deg C; piperazine down; 1 Hoecsht 33258, 1 Mg, and 65 HOHs #1d45 1.9 dimer (a2) - 2 chains given [12]; -25 deg C; piperazine down; 1 Hoecsht 33258, 1 Mg, and 94 HOHs #1d46 2.0 dimer (a2) - 2 chains given [12]; -100 deg C; piperazine down; 1 Hoecsht 33258, 1 Mg, and 91 HOHs #1d64 2.10 dimer (a2) - 2 chains given [12]; 5'-CGCGAATTGCGC-3'; 1 pentami- dine and 77 HOHs #1d80 2.2 dimer (a2) - 2 chains given [12]; 5'-CGCGAATTGGCG-3'; 72 HOHs #1d85 2.5 dimer (a2) - 2 chains given [12]; 5'-CGC+GAATTCGCG-3'; 2 ethyl- ated guanines, 1 netropsin, and 89 HOHs #1d86 2.2 dimer (a2) - 2 chains given [12]; 1 netropsin and 74 HOHs #2dbe 2.5 dimer (a2) - 2 chains given [12]; 1 berenil and 48 HOHs #4dnb 2.0 dimer - 2 chains given [12]; 5'-CGCGA+ATTCGCG-3'; 2 methylated adenines; 87 HOHs #1dnh 2.25 dimer (a2) - 2 chains given [12]; 1 Hoechst 33258 and 126 HOHs #1dnm 2.5 dimer (a2) - 2 chains given [12]; 5'-CGCAAGCTGGCG-3'; 1 spermine (one half molecule) and 47 HOHs #1prp 2.1 dimer (a2) - 2 chains given [12]; 1 propami dine and 69 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGATATCGCG-3' and variants #1dne 2.4 dimer (a2) - 2 chains given [12]; 5'-CGCGATATCGCG-3'; 1 netropsin and 60 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCGCGCGCGCG-3' #2zna --- dimer - 2 chains given [12]; idealized Z-DNA model; probably based on 2dcg; form Z-I #3zna --- dimer - 2 chains given [12]; idealized Z-DNA model; probably based on 2dcg; form Z-II Deoxyribonucleic Acid (DNA) 5'-CGCGAATTCGCG-3' and variants #1d30 2.4 dimer (a2) - 2 chains given [12]; 1 4'-6-diamidine-2-phenyl indole; 26 HOHs #1d75 2.8 dimer (a2) - 2 chains given [12]; 5'-CGCGAATT(+A)GCG-3'; 2 8-oxo- adenines and 67 HOHs Deoxyribonucleic Acid (DNA) 5'-CGCIAATTCGCG-3' #1d77 2.4 dimer (a2) - 2 chains given [12]; 44 HOHs Deoxyribonucleic Acid (DNA) 5'-CGTGAATTCACG-3' #1d28 2.7 dimer (a2) - 2 chains given [12]; 85 HOHs #1d29 2.5 dimer (a2) - 2 chains given [12]; 36 HOHs; solved by different group Deoxyribonucleic Acid (DNA) 5'-CGTAGATCTACG-3' #119d 2.25 dimer - 2 chains given [12]; 1 Mg++ and 137 HOHs Deoxyribonucleic Acid (DNA) 5'-GCCGAATTCGGC-3' #132d NMR dimer - 2 chains given [12]; 1 structure Deoxyribonucleic Acid (Oxytricha) 5'-GGGGTTTTGGGG-3' #1d59 2.50 tetramer (a4) - 4 chains given [12] Deoxyribonucleic Acid (DNA) (HIV-1) 5'-AGCTTGCCTTGAG-3' + 5'-CTCAAGGCAAGCT-3' #140d NMR dimer (ab) - 1 model of 2 chains given [13]; A-DNA starting model; SEQRES records for chain B differ from ATOM records #141d NMR dimer (ab) - 1 model of 2 chains given [13]; B-DNA starting model; SEQRES records for chain B differ from ATOM records #142d NMR dimer (ab) - 1 model of 2 chains given [13]; "final" structure - minimized average; SEQRES records for chain B differ from ATOM records Deoxyribonucleic Acid (DNA) 5'-CTGTAGTGCTCAC-3' #1da4 NMR dimer (ab) - 2 models of 2 chains given[13]; 1 cis-platinum- (NH3)2; "loop in" model #1da5 NMR dimer (ab) - 2 models of 2 chains given[13]; 1 cis-platinum- (NH3)2; "loop out" model Deoxyribonucleic Acid (DNA) 5'-AGATAAACGTTTATCT-3' DUP1gat NMR dsDNA + dimer (d2 + a2) - 2 chains given [16, 60]; minimized average structure; 1 Zn ++ DUP1gau NMR dsDNA + dimer (d2 + a2) - 31 models of 2 chains given [16, 60]; 1 Zn ++ Deoxyribonucleic Acid (DNA) 5'-CGCGCGTTTTCGCGCG-3' #1d16 2.1 dimer (a2) - 1 chain given [16]; 70 HOHs Deoxyribonucleic Acid (DNA) 5'-GCGCGCGCGCGCGCGC-3' #5zna --- dimer (a2) - 2 chains given [16]; model Deoxyribonucleic Acid (DNA) 5'-GGGGGGGGGGGGGGGG-3' #1dn7 --- dimer (ab) - 2 chains given [16]; model Deoxyribonucleic Acid (Synthetic?) 5'-CCGACCGACGTCGGTCG-3' DUP2bop 1.7 dsDNA + virus (d2 + a2) - 2 chains given [17, 85]; protein: DNA- binding domain, residues 325-410; 2 Ybs and 121 HOHs DNA Operator Cro (Phage Lambda) 5'-TATCACCGCGGGTGATA-3' DUP4cro 3.9 CA dsDNA + repressor (d2 + a2) - 12 chains given [17, 66] Glucocorticoid Receptor (Rattus rattus) 5'-CCAGAACATCGATGTTCTG-3' DUP1glu 2.9 dsDNA + receptor (d2 + a2) - 4 chains given [19, 81]; fragment of protein (440 - 525); 4 Zn++s and 41 HOHs GAL4 Recognition Site (DNA) 5'-CCGGAGGACAGTCCTCCGG-3' DUP1d66 2.7 dsDNA + dimer (d2 + a2) - 4 chains given [19, 66]; 4 Cds and 51 HOHs; chain D DNA has one base pair diff from chain E TRP Repressor/Operator (Synthetic) 5'-TGTACTAGTTAACTAGTAC-3' DUP1tro 1.9 dsDNA + dimer (d2 + a2) - 8 chains given [19, 107]; HOHs Deoxyribonucleic Acid (DNA) 5'-ATGGCGCCCGAACAGGGAC-3' DUP1hmi 3.0 CA dsDNA (ab) + HIV RT - 4 chains given [19, 18, 556, 430]; C280S mutant ATF/CREB Site DNA 5'-TGGAGATGACGTCATCTCC-3' DUP1dgc 3.0 dimer + GCN4 zipper (d2 + a2) - 2 chains given [19, 62] DNA Operator (Phage Lambda) 5'-AATACCACTGGCGGTGATAT-3' DUP1lmb 1.8 dsDNA + repressor (d2 + a2) - 4 chains given [20, 92]; super- sedes 1lrd; 140 HOHs DNA Operator OR1 (Phage 434) 5'-AAGTACAAACTTTCTTGTAT-3' DUP3cro 2.5 dsDNA + repressor (d2 + a2) - 4 chains given [20, 71]; 25 HOHs DUP2or1 2.5 dsDNA + repressor (d2 + a2) - 4 chains given [20, 69]; 44 HOHs DNA Operator OR2 (Phage 434) 5'-GACAAACAAGATACATTGTAT-3' DUP1rpe 2.5 dsDNA + repressor (cd + a2) - 4 chains given [21, 19, 69]; 36 HOHs DNA Operator OR3 (Phage 434) 5'-AAGTACAGTTTTTCTTGTAT-3' DUP1per 2.5 dsDNA + repressor (d2 + a2) - 4 chains given [20, 69]; 40 HOHs AP-1 DNA 5'-TTCCTATGACTCATCCAGTT-3' DUP1ysa 2.9 dsDNA + GCN4 (d2 + a2) - 4 chains given [20, 57]; 17 HOHs DNA - Telomeric AG3 Repeat (Homo sapiens) 5'-AGGGTTAGGGTTAGGGTTAGGG-3' #143d NMR monomer [22]; intramolecular quadruplex Deoxyribonucleic Acid Poly-CT/GA (DNA) #1d71 --- dimer (ab) - 2 chains given [47]; 23(GA)-G and complement; "nodule" DNA CAP-DNA (Escherichia coli) 5'-GTCACACTTTTCGGCGAAAAGTGTGACATAT-3' DUP1cgp 3.0 dimer + activator protein (ab + a2) - 4 chains given [31, 205]; 2 cyclic AMPs Deoxyribonucleic Acid (DNA) 5'-TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT-3' #134d NMR trimer? - 1 chain given [31]; minimized average structure 1 #135d NMR trimer? - 1 chain given [31]; minimized average structure 2 #136d NMR trimer? - 14 models of 1 chain given [31]; restrained molecular dynamics Deoxyribonucleic Acid (DNA) 171 bp #1dnn --- dimer (ab) - 2 chains given; model of 171 bp dsDNA DNA Polymerase I Klenow Fragment (Escherichia coli) (1dpi: 1dpi) {domain 1: a/b/a doubly wound para beta} XXX look again {domain 2: a/b misc anti beta} #1dpi 2.8 CA 1 chain [605]; 1 Zn DNA Polymerase Beta (Rattus norvegicus) {domain 1: 9-87: crossed anti alpha pairs} {domain 2: 88-147: crossed alphas} {domain 3: 148-273: a/b/a+open doubly wound mixed beta ud/ud} {domain 4: 274-335: a/b/c doubly wound anti beta ud/cr + alpha} #1bpb 2.3 monomer fragment [248]; minus domain 1; 90 waters #1bpd 3.6 monomer [335]; 1 PO4 #1bpd 3.9 monomer [335]; 1 DTP Dialkylglycine Decarboxylase (Pseudomonas cepacia) {domain 1: 3-61: anti betas + alphas} {domain 2: 62-110,244-325: a/b/a doubly wound anti beta ud + open face anti alphas} {domain 3: 111-243: a/b/a doubly wound para beta ud/ud + coil} {domain 4: 326-433: a/b open face anti beta ud} #1dgd 2.8 tetramer (a4) - 1 chain given [432]; 1 PLP, 1 MES, 1 Na+, 1 Li+, and 99 HOHs #1dge 2.8 tetramer (a4) - 1 chain given [432]; Q15H mutant; 1 PLP, 1 MES, 2 Rb+s, and 94 HOHs #1dka 2.6 tetramer (a4) - 1 chain given [433]; 0M variant; 1 PLP, 1 MES, 1 Na+, 1 K+, and 145 HOHs Dihydrofolate Reductase (Escherichia coli) (4dfr.B: 4dfr.B [3dfr] [8dfr]) {domain 1: 1-38,107-159: a/b/c doubly wound mixed beta ud/cr} {domain 2: 39-106: a/b/a doubly wound para beta ud/ud} [dfr] XXX Thornton dw2 #4dfr 1.7 monomer - 2 chains given [159]; supersedes 2dfr; chain B pre- ferred for structural comparisons; resistant strain; 2 MTXs, 2 Cl-s, 1 Ca++, and 428 HOHs; K154E variant #5dfr 2.3 monomer [159]; apo; resistant strain; 3 Cl-s and 120 HOHs #6dfr 2.4 monomer [159]; resistant strain; 1 NAP+, 1 Ca++, and 72 HOHs #7dfr 2.5 monomer [159]; resistant strain; 1 folate, 1 NAP+, and 55 HOHs #1dhi 1.9 monomer - 2 chains given [159]; D27S mutant; 2 MTXs, 2 Cl-s, 1 Ca++, and 385 HOHs #1dhj 1.8 monomer - 2 chains given [159]; D27S and F137S mutant; 2 MTXs, 2 Cl-s, 1 Ca++, and 404 HOHs #1dra 1.9 monomer - 2 chains given [159]; D27E mutant; isozyme 1; 2 MTXS, 2 Cl-s, 1 Ca++, and 426 HOHs #1drb 1.9 monomer - 2 chains given [159]; D27C mutant; isozyme 1; 2 MTXs 2 Cl-s, 2 ethanols, 1 Ca++, and 426 HOHs #2drc 1.9 monomer - 2 chains given [159]; W22F mutant; chain B preferred; 2 MTXs, 1 Ca++, 2 Cl-s, and 48 HOHs #3drc 1.9 monomer - 2 chains given [159]; 2 MTXs, 2 Cl-s, 1 Ca++, and 377 HOHs Dihydrofolate Reductase (Gallus gallus) (8dfr: 8dfr [3dfr] [4dfr.B]) {domain 1: 1-40,129-186: a/b/c doubly wound mixed beta ud/cr} {domain 2: 41-128: a/b/a doubly wound para beta ud/ud} [dfr] XXX Thornton dw2 #8dfr 1.7 monomer [189]; 1 NADPH, 1 Ca++, and 122 HOHs #1dr1 2.2 monomer [189]; 1 NAP+, 1 1,2-dihydroxypropyl-6-pterin, 1 Ca++, and 133 HOHs #1dr2 2.3 monomer [189]; 1 thio-NADP+, 1 Ca++, and 73 HOHs #1dr3 2.3 monomer [189]; 1 thio-NADP+, 1 1,2-dihydroxypropyl-6-pterin, 1 Ca++, and 110 HOHs #1dr4 2.4 monomer [189]; Cys 11 - modified by methyl Hg; 1 NAP+, 1 Ca++, 1 1,2-dihydroxypropyl-6-pterin, and 76 HOHs #1dr5 2.4 monomer [189]; Cys 11 - modified by methyl Hg; 1 NAP+, 1 Ca++, and 73 HOHs #1dr6 2.4 monomer [189]; 1 mercuric benzoate, 1 NAP+, 1 1,2-dihydroxypro- pyl-6-pterin, 1 Ca++, and 74 HOHs #1dr7 2.4 monomer [189]; 1 mercuric benzoate, 1 NAP+, 1 Ca++, and 56 HOH Dihydrofolate Reductase (Homo sapiens) (1drf: 8dfr [3dfr] [4dfr.B]) {domain 1: 1-40,128-186: a/b/c doubly wound mixed beta ud/cr} {domain 2: 41-127: a/b/a doubly wound para beta ud/ud} [dfr] XXX Thornton dw2 #8dfr 1.7 monomer [189]; 1 NADPH, 1 Ca++, and 122 HOHs #1dr1 2.2 monomer [189]; 1 NAP+, 1 1,2-dihydroxypropyl-6-pterin, 1 Ca++, and 133 HOHs #1dr2 2.3 monomer [189]; 1 thio-NADP+, 1 Ca++, and 73 HOHs #1dr3 2.3 monomer [189]; 1 thio-NADP+, 1 1,2-dihydroxypropyl-6-pterin, 1 Ca++, and 110 HOHs #1dr4 2.4 monomer [189]; Cys 11 - modified by methyl Hg; 1 NAP+, 1 Ca++, 1 1,2-dihydroxypropyl-6-pterin, and 76 HOHs #1dr5 2.4 monomer [189]; Cys 11 - modified by methyl Hg; 1 NAP+, 1 Ca++, {a/b/a doubly wound para beta} [dfr] #1dhf 2.3 monomer - 2 chains given [186]; 2 folates and 116 HOHs #2dhf 2.3 monomer - 2 chains given [186]; 2 5-deazafolates and 116 HOHs #1drf 2.0 monomer [186]; recombinant form; 1 folate, 2 SO4s, and 249 HOHs Dihydrofolate Reductase (Lactobacillus casei) (3dfr: 3dfr [4dfr.B] [8dfr]) {domain 1: 1-34,110-162: a/b/c doubly wound mixed beta ud/cr} {domain 2: 35-109: a/b/a doubly wound para beta ud/ud} [dfr] XXX Thornton dw2 #3dfr 1.7 monomer [162]; supersedes 1dfr; 1 NADPH, 1 MTX, and 264 HOHs Dihydrolipoamide Dehydrogenase (Azotobacter vinelandii) (3lad.A: 3lad.A [3grs] [2tpr.A] [1lvl] [1npx]) {domain 1: 1-151,281-348: a/b/b doubly wound para beta ud/cr + anti alpha} {domain 2: 152-280: a/b/b doubly wound para beta ud/cr} *good for structure picture {domain 3: 349-480: a/b/a doubly wound anti beta ud/ud} #3lad 2.2 dimer (a2) - 2 chains given [476]; 2 FADs and 451 HOHs; 2 SSs Dihydrolipoamide Dehydrogenase (Pseudomonas putida) (1lvl: 1lvl [3grs] [3lad.A] [2tpr.A] [1npx]) {domain 1: 1-147,266-335: a/b/b doubly wound para beta ud/cr + anti alpha} {domain 2: 148-265: a/b/b doubly wound para beta ud/cr} {domain 3: 336-458: a/b/a doubly wound anti beta ud/ud} #1lvl 2.45 dimer (a2) - 1 chain given [458]; 1 FAD, 1 NAD, and 190 HOHs; 1 SS Dihydrolipoamide Succinyltransferase (Escherichia coli) (1bbl: 1bbl) {up down para alpha + coil} #1bal NMR monomer - 56 models given [51]; E3 binding domain - from 2-oxo- glutarate dehydrogenase multienzyme complex #1bbl NMR monomer [51]; energy minimized average; E3 binding domain - from 2-oxoglutarate dehydrogenase multienzyme complex Dihydrolipoyl Transacetylase (Azotobacter vinelandii) (1eaf: 1eaf) {a/b/c doubly wound mixed beta ud/ud + alphas + anti beta} #1eaa 2.6 24mer - 1 chain given [243]; catalytic domain; 37 HOHs #1eab 2.6 24mer - 1 chain given [243]; catalytic domain; 1 ACO, 1 lipo- amide, 42 HOHs #1eac 2.6 24mer - 1 chain given [243]; catalytic domain; 1 ACO, 1 dithio- theitol, and 36 HOHs #1ead 2.6 24mer - 1 chain given [243]; catalytic domain; 1 ACO and 45 HOHs #1eae 3.0 24mer - 1 chain given [243]; catalytic domain; 1 lipoamide and 30 HOHs #1eaf 2.3 24mer - 1 chain given [243]; catalytic domain; 1 hydrogen sul- fite and 147 HOHs Dihydropteridine Reductase (Homo sapiens) {a/b/a doubly wound para beta ud/ud + anti beta + alpha} #1hdr 2.5 tetramer? - 1 chain given [244]; 1 NAD and 91 HOHs Dihydropteridine Reductase (Rattus norvegicus) (1dhr: 1dhr) {a/b/a doubly wound para beta ud/ud + anti beta + alpha} #1dhr 2.3 monomer? [241]; 1 NADH and 136 HOHs #1dir 2.6 tetramer? - 4 chains given [241]; 4 NADs and 148 HOHs Diphtheria Toxin (Corynebacterium diphtheriae) {domain 1: 4-144,274-294: a/a/c doubly wound mixed alpha} {domain 2: 145-273: encircled axial alpha + anti betas} #1ddt 2.0 dimer (a2) - 1 chain given [535]; 1 APU + 405 HOHS Disulfide Bond Formation Protein (Escherichia coli) (1dsb.A: 1dsb.A) {domain 1: 1-60,147-188: a/b open face mixed beta} {domain 2: 61-146: a/a/a doubly wound para alpha ud/cr} #1dsb 2.0 monomer? - 2 chains given [189]; 195 HOHs; 2 SSs E42 Protein Product of Gene E2A (Homo sapiens) (1hlh.A: 1hlh.A) {up down anti alpha} #1hlh --- dimer? (a2) - 2 chains given [64]; helix-loop-helix motif; non- experimental model Echistatin (Echis carinatus) (2ech: 2ech [1kst]) {SS rich anti beta + coil} #2ech NMR monomer? - 8 models given [50]; 1 terminal amide; 4 SSs EcoRI Endonuclease (Escherichia coli) (1r1e.E: 1r1e.E) {domain 1: 17-115,141-171,200-277: a/b doubly wound mixed beta ud/ud + anti beta + alpha} {domain 2: 116-140,172-199: a/b open face anti beta ud} #1r1e 2.7 CA dimer + dsDNA (a2 + d2) - 2 chains given [276, 13] EcoRV Endonuclease (Escherichia coli) (1rve.A: 1rve.A) {domain 1: 2-203: a/b/abc doubly wound mixed beta ud/ud+cr + anti betas} {domain 2: 204-245: crossed alpha + alpha} #1rve 2.5 dimer (a2) - 2 chains given [245]; 49 HOHs #2rve 3.0 dimer + dsDNA (a2 + d4) - 6 chains given [244, 8]; DEL M1; 68 HOHs #4rve 3.0 dimer + dsDNA 1.5*(a2 + d2) - 6 chains given [244, 10]; DEL M1; 23 HOHs Eglin C (Hirudo medicinalis) (1egl: 1egl [2ci2.I]) {a/b/c doubly wound para beta ud/ud + anti beta} [eglin] DUP1acb 2.0 inhibitor + alpha chymotrypsin - 2 chains given [70, 245]; N33D variant; 142 HOHs DUP1cse 1.2 inhibitor + protease subtilisin [71, 274]; 2 Ca++s and 432 HOHs #1egl NMR monomer - 25 models given [70]; N33D variant DUP1mee 2.0 inhibitor + mesentericopeptidase - 2 chains given [64, 275]; part of seq missing; 2 Cas and 312 HOHs DUP1sbn 2.1 inhibitor + subtilisin Novo - 2 chains given [70, 274]; L45R mutant; part of seq missing; 2 Ca++s and 316 HOHs DUP2sec 1.8 inhibitor + protease subtilisin [71, 274]; 3 Ca++s and 170 HOHs DUP1sib 2.4 inhibitor + protease subtilisin (i + a) - 2 chains given [70, 275]; R53K mutant; 2 Ca++s and 195 HOHs DUP1tec 2.2 inhibitor + protease thermitase [70, 279]; N33D variant; 2 Ca++s, 1 Na+, and 208 HOHs DUP2tec 1.98 inhibitor + protease thermitase [70, 279]; N33D variant; 5 mM Ca; 2 Ca++s, 1 Na+, and 224 HOHs DUP3tec 2.0 inhibitor + protease thermitase [70, 279]; N33D variant; 100 mM Ca; 3 Ca++s and 130 HOHs Elastase, Human Leukocyte (Neutrophil) (Homo sapiens) (1hne.E: 1hne.E [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1sgt] [1ton]) {domain 1: 16-27,129-231: Greek anti beta} {domain 2: 28-128,232-243: Greek anti beta + alpha} [s_prot+] #1hne 1.84 monomer + inhibitor [218, 4]; 1 methoxysuccinyl-Ala-Ala-Pro-Ala- chloromethyl inhibitor; 225 HOHs #1ppf 1.8 monomer + ovomucoid inhibitor - 2 chains given [218, 56]; D78N diff vs 1hne; 6 NAGs, 2 FUCs, 6 MANs, 2 GLCs, and 272 HOHs; 7 SSs #1ppg 2.3 monomer + inhibitor [218, 5]; D78N diff vs 1hne; 1 methoxysuc- cinyl-Ala-Ala-Pro-Ala-chloromethyl inhibitor, 6 NAGs, 2 FUCs, 6 MANs, 2 GLCs, and 192 HOHs; 4 SSs Elastase (Pseudomonas aeruginosa) (1ezm: 1ezm [8tln]) {domain 1: 1-151: a/b/c doubly wound mixed beta ud/cr + anti beta} {domain 2: 152-298: crossed + schief alpha} [tln+] #1ezm 1.5 monomer [301]; 1 Zn++, 1 Ca++, and 157 HOHs; 2 SSs Elastase (Sus Scrofa) (3est: 3est [2cga.A] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: 16-24,129-231: Greek anti beta} {domain 2: 25-128,232-245: Greek anti beta + alpha} [s_prot+] #1ela 1.8 monomer + peptide - 2 chains given [240, 4]; 1 TFA, 1 ISO, 1 Ca++, 1 SO4, 1 ACY, and 166 HOHs; 4 SSs #1elb 2.1 monomer + peptide - 2 chains given [240, 4]; 1 TFA, 1 ISO, 1 Ca++, 1 SO4, and 126 HOHs; 4 SSs #1elc 1.75 monomer + peptide - 2 chains given [240, 4]; 1 TFA, 1 ISO, 1 Ca++, and 130 HOHs; 4 SSs #1esa 1.65 monomer [240]; low temp form -45 C; 1 Ca++, 2 SO4s, and 134 HOHs; 4 SSs #1esb 2.3 monomer [241]; low temp form; 1 CBZ, 1 Ca++, 1 SO4, and 126 HOHs; 4 SSs #1est 2.5 monomer [240]; 1 SO4 S, 1 p-toluenesulfonyl derivative of serine, and 25 HOHs; 4 SSs #2est 2.5 monomer + inhibitor [240, 4]; 1 trifluoroacetyl-L-lysyl-L-alanyl- P-trifluoromethyl-phenylanilide, 1 SO4, 45 HOHs; 4 SSs #3est 1.65 monomer [240]; native; 1 Ca++, 2 SO4s, and 129 HOHs; 4 SSs #4est 1.78 monomer + inhibitor - 2 chains given [240, 5]; 1 peptide with 1,1-difluoro-N-phenylethyl acetamide, 1 Ca++, 1 SO4, and 156 HOHs; 4 SSs #5est 2.09 monomer + inhibitor - 2 chains given [240, 3]; 1 carbobenzoxy- alanyl-isoleucylboronic acid, 1 Ca++, 1 SO4, and 202 HOHs; 4 SSs #6est 1.8 monomer [240]; crystallized in 10% dimethylformamide with pH 5.3 acetate buffer; 3 DMFs, 1 Ca++, 1 SO4, and 114 HOHs; 4 SSs #7est 1.8 monomer + inhibitor - 2 chains given [240, 4]; crystallized in 10% dimethylformamide with pH 5.3 acetate buffer; 1 trifluoro- acetate, 1 trifluoromethylphenylanilide, 5 DMFs, 1 Ca++, 1 SO4, and 103 HOHs; 4 SSs #8est 1.78 monomer [240]; 1 4-chloro-3-ethoxy-7-guanidino-isocoumarin, 1 SO4, 1 Ca++, and 169 HOHs; 4 SSs #9est 1.9 monomer [240]; 1 (1-bromoethyl)(2'-formyl-4'-amino-phenyl)ace- tate, 1 SO4, 1 Ca++, and 169 HOHs; 4 SSs #1inc 1.94 monomer [240]; 1 (1-(5-chloro-4-oxo-4H-3,1-benzoxazine-2-yl)-2- methyl-propyl) carbamic acid 1,1-dimethylethyl ester, 1 SO4, 1 Ca++, and 141 HOHs; 4 SSs #1jim 2.31 monomer [240]; 1 methyl 2-acetoxy-2-(2-carboxy-4-amino-phenyl) acetate, 1 SO4, and 133 HOHs; 4 SSs Elongation Factor TU (Escherichia coli B) (1etu: 1etu) {a/b/a doubly wound para beta ud/ud} [etu] XXX Thornton dw1 #1efm 2.7 CA 1 chain [393]; trypsin modified; excised residues labeled EXC; 1 Mg and 1 GDP; C terminus S vs. G in 1etu #1etu 2.9 monomer [394]; domain I (part of molecule not included in data set); 1 GDP and 1 Mg; excised residues labeled EXC Elongation Factor TU (Thermus Aquaticus) {domain 1: 1-212: a/b/a doubly wound para beta ud/ud} [etu+] {domain 2: 213-311: Greek anti beta} XXX {domain 3: 312-405: Greek anti beta} #1eft 2.5 monomer [405]; 1 GNP, 1 Mg++, and 126 HOHs Endo-1,4-Beta-D-Glucanase (Thermomonospora fusca, strain YX) (1tml: 1tml [3cbh]) {a/b singly wound para beta + anti alpha + crossed alpha} #1tml 1.8 monomer [286]; true C-terminus not known; 1 SO4 and 73 HOHs; 2 SSs Endo-1,4-Beta-D-Glucanase (Clostridium thermocellum) Endochitinase (Hordeum vulgare l.) (2baa: 2baa) {encircled axial alpha + anti beta} *good for structure picture XXX***Show this one to Cynthia #2baa 1.8 monomer? [243]; 3 SSs Endoglucanase V (Humicola insolens) {Greek anti beta + coil + alphas} XXX #1eng 1.6 CA monomer? [213] Endonuclease III (Escherichia coli) (1abk: 1abk) {domain 1: 1-21,132-211: wedge alpha with end alpha + crossed alpha + metal rich coil} {domain 2: 22-103: a/a/a doubly wound para alpha ud/cr} {domain 3: 104-131: crossed alpha} {domain 2: metal rich Greek anti alpha} #1abk 2.0 monomer? [211]; 1 FS4 and 118 HOHs Endonuclease V (Bacteriophage T4) (2end: 2end) {anti alpha + coil + crossed alpha + anti beta} XXX Cynthia look #2end 1.45 monomer [138]; 172 HOHs; supersedes 1end #1eni 2.2 monomer [138]; R3Q mutant; 111 HOHs #1enj 1.8 monomer [138]; E23Q mutant; 98 HOHs #1enk 2.0 monomer [138]; E23D mutant; 109 HOHs Endothiapepsin (Endothia parasitica) (4ape: 2apr [3psg] [1smr.A] [1lya.B] [1mpp]) {domain 1: -2-174: multiple anti beta} [ac_prot] {domain 2: 175-326: multiple anti beta} [ac_prot] or {domain 1: 1-13,139-187,307-325: c/b open face anti beta + alpha} {domain 2: 17-139: multiple anti beta} reverse s with caps XXX {domain 3: 188-306: Greek anti beta + anti beta} XXX Thornton twisted sheet #4ape 2.1 monomer [330]; 342 HOHs; 1 SS #1eed 2.0 monomer + inhibitor - 2 chains given [330, 4]; 1 tert-butyloxy- carbonyl, 1 1-hydroxy-3-phenylalanine-propylene, 1 1-hydroxy-3- phenylalanine-ethylene, and 278 HOHs; 1 SS #1ent 1.9 monomer + inhibitor PD130328 - 2 chains given [330, 5]; 1 tert- butyloxycarbonyl, 1 phophostatine, 1 decarboxy-isoleucine, 2 SO4s, and 265 HOHs; 1 SS #1er8 2.0 monomer + inhibitor H-77 [330, 8]; 67 HOHs; 1 SS #2er0 3.0 monomer + inhibitor L364,099 [330, 9]; 1 isovaleric acid, 1 5- cyclohexyl-4-amino-3-hydroxy pentanoic acid, and 1 terminal amide; 1 SS #2er6 2.0 monomer + inhibitor H-256 [330, 7]; 321 HOHs; 1 SS #2er7 1.6 monomer + inhibitor H-261 [330, 8]; 3 SO4s and 321 HOHs; 1 SS #2er9 2.2 monomer + inhibitor L363,564 [330, 9]; 322 HOHs; 1 SS #3er3 2.0 monomer + inhibitor CP-71,362 [330, 6]; 246 HOHs; 1 SS #3er5 1.8 monomer + inhibitor H-189 [330, 10]; 1 statine and 223 HOHs; 1 SS #4er1 2.0 monomer + inhibitor PD125967 [330, 4]; 260 HOHs; 1 SS #4er2 2.0 monomer + inhibitor pepstatin [330, 6]; 3 SO4s and 343 HOHs; 1 SS #4er4 2.1 monomer + inhibitor H-142 [330, 10]; 325 HOHs; 1 SS #5er1 2.0 monomer + inhibitor BW624 [330, 6]; 1 leucinol, 1 methylene, 1 methoxy, and 330 HOHs; 1 SS #5er2 1.8 monomer + inhibitor CP-69,799 [330, 6]; 1 tert-butyloxycarbonyl anion, 1 N-isobutyl-N-carboxy-2-hydroxy-3-amino-4 246 HOHs; 1 SS Engrailed Homeodomain (Drosophila melanogaster) (1hdd.C: 1hdd.C [2hoa]) {a/a open face anti alpha} XXX twisted up down #1enh 2.1 monomer [54]; 33 HOHs #1hdd 2.8 monomer + monomer + dsDNA - 4 chains given [61, 21] Enolase (2-Phospho-D-Glycerate Hydrolase) (Saccharomyces cerevisiae) (4enl: 4enl) {domain 1: 1-128: open face anti beta + anti alpha} or {domain 1: 1-128: a/a/b doubly wound para alpha ud/cr} XXX {domain 2: 129-436: a/b singly wound para beta} #1els 2.4 dimer (a2) - 1 chain given [436]; 1 Mn, 1 PAH, and 343 HOHs #3enl 2.25 dimer (a2) - 1 chain given [436]; supersedes 2enl; apo; 1 SO4 and 353 HOHs #4enl 1.9 dimer (a2) - 1 chain given [436]; holo; 1 Zn++, 1 SO4, and 348 HOHs #5enl 2.2 dimer (a2) - 1 chain given [436]; 1 Ca++, 1 2-phospho-D-glyceric acid, and 355 HOHs #6enl 2.2 dimer (a2) - 1 chain given [436]; 1 Zn++, 1 phosphoglycolic acid, and 344 HOHs #7enl 2.2 dimer (a2) - 1 chain given [436]; 1 Mg++, 1 2-phospho-D-glyceric acid, and 347 HOHs #1nel 2.6 dimer (a2) - 1 chain given [436]; 1 Mg++, 1 phosphate, 1 F-, and 274 HOHs 5-Enol-Pyruvyl-3-Phosphate Synthase (Escherichia coli) (1eps: 1eps) {domain 1: 19-240: 3 X a/b open face anti beta with para alpha inside} {domain 2: 1-18,241-427: 3 X a/b open face anti beta with para alpha inside} #1eps 3.0 CA monomer? [427] Epidermal Growth Factor (Mus musculus) (1epg: 1epg) {SS rich c/b open face anti beta + anti beta} #1egf NMR monomer - 16 models given [53]; 3 SSs #3egf NMR monomer - 16 models given [53]; after energy minimization; 3 SSs #1epg NMR monomer [53]; pH 2; minimized mean structure; preferred structure for modeling use (over 1epi); 3 SSs #1eph NMR monomer - 10 models given [53]; pH 2; 3 SSs #1epi NMR monomer [53]; pH 6.8; minimized mean structure; 3 SSs #1epj NMR monomer - 5 models given [53]; pH 6.8; 3 SSs Equine Herpes Virus-1 (Equine Herpes Virus-1) {metal rich a/b open face anti beta + coil} #1chc NMR fragment [68]; C3HC4 domain; 2 Zn++s Equine Infections Anemia Virus Protease (Equine Infections Anemia Virus) #1eqi --- dimer (a2) + peptide - 3 chains given [104, 10]; theoretical model; 1 NH2 and 1 HOH Erabutoxin (Laticauda semifasciata) (3ebx: 3ebx [1cdt.A] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich c/b open face anti beta cr + anti beta} [tox] #1nxb 1.38 monomer [62]; B; H6Q and Q7H; 4 SSs #3ebx 1.4 monomer [62]; B; supersedes 2ebx; 1 SO4 and 111 HOHs; 4 SSs #5ebx 2.0 monomer [62]; A; H62N; 1 SO4 and 62 HOHs; 4 SSs #6ebx 1.7 dimer (a2) - 2 chains given [62]; B; 1 SCN- and 97 HOHs; 8 SSs #1era NMR monomer [62]; B; minimized average structure #1fra NMR monomer - 14 models given [62]; B; 4 SSs Erythroid Transcription Factor GATA-1 (Gallus gallus) (1gat.A: 1gat.A) {anti beta + alpha + coil} #1gat NMR dimer + dsDNA (a2 + d2) - 2 chains given [60, 16]; minimized average structure; 1 Zn ++ #1gau NMR dimer + dsDNA (a2 + d2) - 30 models of 2 chains given [60, 16]; 1 Zn ++ E-Selectin (Homo sapiens) #1esl 2.0 monomer? [162]; 3 Ca++s, 2 Cl-s, and 112 HOHs; 5 SSs Endothelin 1 (Synthetic) (1edp: 1edp) {SS rich alpha + coil} #1edp NMR monomer [17]; minimized best conformer; 2 SSs Factor H (Homo sapiens) (1hfh: 1hfh) {domain 1: SS rich up down anti beta} {domain 2: SS rich up down anti beta} #1hcc NMR monomer [59]; energy minimized average structure; 16th complement control protein; contains one artifactual cis peptide bond; 2 SSs #1hfh NMR monomer? [120]; 15th and 16th C-module pair; minimum averaged structure #1hfi NMR monomer? [62]; 15th C-module pair; minimum averaged structure Factor IX (Homo sapiens) (1ixa: 1apo) {SS rich c/b open face anti beta} #1ixa NMR fragment [38]; minimized average structure; 3 SSs Fasciculin 1 (Dendroaspis angusticeps) (1fas: 1fas [3ebx] [1cdt.A] [1nbt.A] [2abx.A] [2ctx]) {SS rich c/b open face anti beta ud + anti beta} [tox+] #1fas 1.8 monomer? [61]; 105 HOHs; 4 SSs Fatty Acid Binding Protein (Homo sapiens) (2hmb: 2hmb [1icm] [1opb.A] [1mdc]) {up down anti beta + schief alpha} #2hmb 2.1 monomer [132]; holo; 1 1-hexyldecanoic acid and 54 HOHs Fatty Acid Binding Protein (Manduca sexta l.) (1mdc: 1mdc [1icm] [1opb.A] [2hmb]) {up down anti beta + schief alpha} #1mdc 1.75 monomer? [132]; 1 palmitate, 1 SO4, and 70 HOHs Intestinal Fatty Acid Binding Protein (Rattus rattus and Rattus norvegicus) (1ifb: 1icm [1opb.A] [2hmb] [1mdc]) {up down anti beta + schief alpha} XXX Thornton orthogonal barrel #1icm 1.5 monomer? [131]; holo; 1 myristate and 130 HOHs #1icn 1.74 monomer? [131]; R106Q mutant; holo; 1 oleate and 133 HOHs #1ifb 1.96 monomer [131]; apo, form 1; 52 HOHs #2ifb 2.0 monomer [131]; holo; 1 palmitic acid and 61 HOHs #1ifc 1.19 monomer [132]; apo, form 2; file contains coordinates for two superposed structures Felix (designed protein) (3flx: 3flx) {up down anti alpha} #1flx --- monomer [79]; model; set disulfides and helix distance #3flx --- monomer [79]; model 2; modeled after hemerythrin Ferredoxin (Azotobacter vinelandii) (5fd1: 5fd1 [1fdx]) {metal rich a/b/c doubly wound anti beta ud/cr + alpha + coil} [ferredox] XXX Thornton beta open sandwich #5fd1 1.9 monomer [106]; supersedes 4fd1; 1 FS4, 1 FS3, and 30 HOHs #1fd2 1.9 monomer [106]; C20A mutant; 1 FS4, 1 FS3, and 31 HOHs #2fd2 1.9 monomer [106]; C24A mutant; 1 FS4, 1 FS3, and 30 HOHs #1fda 2.1 monomer [106]; oxidized; pH 6.0; 1 FS4, 1 FS3, and 36 HOHs #1fdb 2.2 monomer [106]; reduced; pH 6.0; 1 FS4, 1 FS3, and 23 HOHs #1fdc 2.1 monomer [106]; reduced; pH 8.0; 1 FS4, 1 FS3, and 25 HOHs #1fdd 1.9 monomer [106]; D15N mutant; 1 FS4, 1 FS3, and 23 HOHs #1fer 2.3 monomer [106]; pH 6.5; 1 FS4, 1 FS3, and 98 HOHs #1frh 2.3 monomer [106]; F2Y mutant; 1 FS4, 1 FS3, and 22 HOHs #1fri 2.1 monomer [106]; D23N mutant; 1 FS4, 1 FS3, and 30 HOHs #1frj 2.3 monomer [106]; F25I mutant; 1 FS4, 1 FS3, and 27 HOHs #1frk 2.1 monomer [106]; H35D mutant; 1 FS4, 1 FS3, and 32 HOHs #1frl 2.3 monomer [106]; E38S mutant; 1 FS4, 1 FS3, and 33 HOHs #1frm 2.3 monomer [106]; E46A mutant; 1 FS4, 1 FS3, and 27 HOHs #1frx 2.5 monomer [106]; C20S mutant; 1 FS4, 1 FS3, and 22 HOHs Ferredoxin (Bacillus thermoproteolyticus) (2fxb: 2fxb [1fxd]) {metal rich a/b open face anti beta ud} [ferredox] XXX Thornton beta open sandwich #2fxb 2.3 monomer [81]; supersedes 1fxb; 1 FS4 and 59 HOHs Ferredoxin (Clostridium acidiurici) {metal rich a/b open face anti beta ud} #1fdn 1.84 monomer [55]; 2 FS4s and 46 HOHs Ferredoxin (Cyanobacterium anabaena) (1fxa.A: 1frr.A) {metal rich ac/b open face anti beta cr + anti beta + alpha} [fxc+] #1fxa 2.5 monomer - 2 chains given [98]; 2 Fe2-S2 clusters and 234 HOHs Heterocyst Ferredoxin (Cyanobacterium anabaena, strain 7120) {metal rich ac/b open face anti beta cr + anti beta + alpha} #1frd 1.7 monomer [98]; oxidized; 1 FES and 58 HOHs Ferredoxin (Equisetum arvense) (1frr.A: 1frr.A) {metal rich a/b open face anti beta cr + anti beta + alpha} [fxc+] #1frr 1.8 monomer - 2 chains given [95]; 2 Fe2-S2s and 183 HOHs Ferredoxin (Peptococcus aerogenes) (1fdx: 1fdx [5fd1]) {metal rich a/b open face anti beta ud} [ferredox] XXX Thornton beta open sandwich #1fdx 2.0 monomer [54]; 2 FS4 s Ferredoxin (Spirulina platensis) (3fxc: 1frr.A) {metal rich a/b open face anti beta cr + coil} [fxc+] #3fxc 2.5 monomer [98]; supersedes 1fxc; 1 Fe2-S2 Ferredoxin I (Aphanothece sacrum) (1fxi.A: 1frr.A) {metal rich a/b open face anti beta cr + coil} [fxc+] XXX Thornton twisted beta 2 or {metal rich double stranded beta cylinder + a/b open face anti beta cr + coil} #1fxi 2.2 monomer - 4 chains given [96]; 4(Fe2-S2)s and 158 HOHs Ferredoxin II (Desulfovibrio gigas) (1fxd: 1fxd [2fxb]) {metal rich a/b open face anti beta} [ferredox+] XXX Thornton beta open sandwich #1fxd 1.7 monomer [58]; 1 SD-CE bonded to SG of Cys 11, 1 FS3, and 56 HOHs; 1 SS Ferredoxin Chloroplastic Transit Peptide (Chlamydomonas reinhardtii) {wedge alpha over coil} XXX good for structure picture #1fct NMR fragment - 32 models given [32] Ferredoxin NADP+ Oxidoreductase (Spinacia oleracea) (1fnr: 1fnr) {domain 1: 19-159: greek anti beta} XXX {domain 2: 160-315: a/b/a(wedges) doubly wound para beta ud/ud} #1fnr 2.2 monomer [314]; 1 FAD #2fnr 3.0 monomer [314]; 1 FAD and 1 2'-phospho-5'-AMP Ferritin (Homo sapiens) (1fha: 1fha) {up down anti alpha + crossed alpha + coil} #1fha 2.4 24-mer - 1 chain given [183]; K86Q mutant; 1 Fe, 2 Cas, and 20 HOHs Fibroblast Growth Factor (Bos taurus) (1bar.A: 4fgf) {6 anti beta pairs on cube faces} crossed XXX 1tie #1afc 2.7 monomer - 8 chains given [140]; C47A mutant; 8 sucrose octa- sulfates #1bar 2.7 monomer - 2 chains given [140]; C47A and H93G mutant; acidic; 36 HOHs Acidic Fibroblast Growth Factor (Homo sapiens) {6 anti beta pairs on cube faces} crossed XXX 1tie #1afg 2.0 monomer - 4 chains given [140]; 4 SO4s and 40 HOHs Basic Fibroblast Growth Factor (Homo sapiens) (4fgf: 4fgf) {6 anti beta pairs on cube faces} crossed XXX 1tie #1bas 1.9 monomer [154]; C70S and C88S mutant; basic; 40 HOHs #1bfg 1.6 monomer [144?]; C69S and C87S mutant; basic; 99 HOHs #2bfh 2.5 monomer [128]; wt; 63 HOHs #1fga 2.2 monomer [146]; expressed in E. coli; 2 SEOs, 2 selenates and 65 HOHs #2fgf 1.77 monomer [146]; expressed in E. coli; 3 SO4s and 67 HOHs #4fgf 1.6 monomer [146]; supersedes 3fgf; expressed in S. cerevisiae; C69 and C92 have bonded SEO; 1 SO4 and 70 HOHs Fibronectin (Homo sapiens) (1ttg: 1ttg) {Greek anti beta} 3 loop #1fna 1.8 fragment [91] #1ttf NMR fragment - 36 models given [94]; tenth type III module #1ttg NMR fragment [94]; tenth type III module; minimized average structure Fibrinopeptide A (Homo sapiens) (1fph.I: 5hir) {coil} DUP1fph 2.5 fragment + thrombin + hirudin fragment - 4 chains given [12, 36, 259, 12]; 1 methylene and 168 HOHs; 4 SSs FIS Protein - Factor for Inversion Stimulation (Escherichia coli) (1fia.A: 1fia.A) {crossed alpha} XXX twisted up down #1fia 2.0 dimer (a2) - 2 chains given [98]; N-terminus poorly defined - residues omitted; 82 HOHs #3fis 2.3 dimer (a2) - 2 chains given [98]; 29 HOHs #4fis 2.3 dimer (a2) - 2 chains given [98]; R89C mutant; 32 HOHs 12 KDa FK-506 Binding Protein (Saccharomyces cerevisiae) (1yat: 1fkf) {a/b open face anti beta + alpha} #1yat 2.5 monomer [113]; 1 FK-506 and 41 HOHs FK-506 Binding Protein (Homo sapiens) (1fkf: 1fkf) {a/b open face anti beta + alpha} #1fkb 1.7 monomer [107]; recombinant form; 1 rapamycin and 133 HOHs #1fkd 1.72 monomer [107]; 1 18-hydroxyascomycin antagonist and 64 HOHs #2fke 1.72 monomer [107]; 1 FK-506 and 71 HOHs #1fkf 1.7 monomer [107]; recombinant form; 1 FK-506 immunosuppressant and 79 HOHs #1fkg 2.0 monomer [107]; 1 (1R)-1,3-diphenyl-1-propyl (2S)-1-(3,3-dimethyl- 1,2-dioxopentyl)-2-piperidinecarboxylate and 87 HOHs #1fkh 1.95 monomer [107]; 1 (1R)-1-cyclohexyl-3-phenyl-1-propyl (2S)-1-(3,3- dimethyl-1,2-dioxopentyl)-2-piperidinecarboxylate and 117 HOHs #1fki 2.2 monomer - 2 chains given [107]; 2 (21S)-1-aza-4,4-dimethyl-6,19- dioxa-2,3,7,20-tetraoxobicyclo[19.4.0]pentacosanes and 111 HOHs #1fkr NMR monomer - 20 models given [107]; recombinant form #1fks NMR monomer [107]; minimized average structure, excluding electro- static interactions; recombinant form #1fkt NMR monomer [107]; minimized average structure, including electro- static interactions; recombinant form Flavocytochrome B2 (Saccharomyces cerevisiae) (1fcb.A.1: 1fcb.A.1 [3b5c]) (1fcb.A.2: 1fcb.A.2 [1gox]) {domain 1: 1-97: heme binding up down anti alpha + a/b open face anti beta ud} [cytb] {domain 2: 98-511: a/b singly wound para beta + anti alpha sheet + anti beta cap} [barrel] #1fcb 2.4 tetramer (a4) - 2 chains given [511]; 1 HEM with Fe++, 2 FMNs, 1 pyruvic acid, and 283 HOHs Flavocytochrome C Sulfide Dehydrogenase (Chromatium vinosum) {domain 1: A1-A38,A59-A109,A256-A401: a/b/b doubly wound para beta ud/cr + open face anti beta} {domain 2: A39-A58,A110-A255: a/b/b doubly wound para beta ud/cr} {domain 3: C1-C174: heme-binding Greek anti alpha} XXX #1fcd 2.53 dimer? (ab) - 4 chains given [401, 174]; 2 FADs, 2 HEMs with Fe++; 2 SSs Flavodoxin (Anabaena 7120) (1flv: 1ofv [2fx2] [2fcr] [4fxn]) {a/b/a doubly wound para beta ud/ud} [nbd+] #1flv 2.0 monomer? [168]; 1 FMN and 104 HOHs Flavodoxin (Anacystis nidulans) (1ofv: 1ofv [2fx2] [2fcr] [4fxn]) {a/b/a doubly wound para beta ud/ud} [nbd+] #1ofv 1.7 monomer? [169]; oxidized; 1 FMN and 89 HOHs Flavodoxin (Chondrus crispus) (2fcr: 2fcr [1ofv] [2fx2] [4fxn]) {a/b/a doubly wound para beta ud/ud} [nbd+] XXX Thornton dw1 #2fcr 1.8 monomer [173]; oxidized; 1 FMN and 110 HOHs Flavodoxin (Clostridium MP) (4fxn: 4fxn [2fx2] [1ofv] [2fcr]) {a/b/a doubly wound para beta ud/ud} [nbd] XXX Thornton dw1 #3fxn 1.9 monomer [138]; oxidized form; supersedes 1fxn; 1 FMN #4fxn 1.8 monomer [138]; semiquinone form; 1 FMN Flavodoxin (Desulfovibrio vulgaris) (2fx2: 2fx2 [1ofv] [2fcr] [4fxn]) {a/b/a doubly wound para beta ud/ud} [nbd] XXX Thornton dw1 #1fx1 2.0 monomer [148]; 1 FMN #2fx2 1.9 monomer [147]; 4 residues differ from 1fx1; 1 FMN and 130 HOHs #3fx2 1.9 monomer [147]; seq as 2fx2; low temp (-150C); oxidized; 1 FMN and 253 HOHs #4fx2 1.9 monomer [147]; seq as 2fx2; low temp (-150C); reduced; 1 FMN and 226 HOHs #5fx2 1.9 monomer [147]; seq as 2fx2; low temp (-150C); fully reduced (hydroquinone); 1 FMN and 244 HOHs Foot and Mouth Disease Virus (Hampster virus) (1bbt.1: 1bbt.1) {double stranded beta cylinder + alpha} (1bbt.2: 1bbt.2 [1tme.2] [2plv.2]) {double stranded beta cylinder + alpha} (1bbt.3: 1bbt.3 [1tme.3] [4rhv.3] [2plv.3]) {double stranded beta cylinder + alpha} (1bbt.4: 1bbt.4) {alpha + coil} #1bbt 2.6 240mer (60abcd) - 4 chains given [213, 218, 220, 85] #1fod 2.6 240mer (60abcd) - 4 chains given [213, 218, 220, 85] Foot and Mouth Disease Virus Type C-S8C1 (Hampster virus) (1fmd.1: 1bbt.1) {double stranded beta cylinder + alpha} (1fmd.2: 1bbt.2 [1tme.2] [2plv.2]) {double stranded beta cylinder + alpha} (1fmd.3: 1bbt.3 [1tme.3] [4rhv.3] [2plv.3]) {double stranded beta cylinder + alpha} (1fmd.4: 1bbt.4) {alpha + coil} #1fmd 3.5 multimer? (Nabcd) - 4 chains given [208, 218, 219, 85] Fructose-1,6-Bisphosphatase (Sus scrofa) (5fbp.A: 5fbp.A) {domain 1: 6-199: a/b open face anti beta ud} {domain 2: 200-338: a/b/a doubly wound mixed beta ud/ud} #1fbc 2.6 tetramer (a4) - 2 chains given [335]; 2 2,5-anhydroglucitol- 1,6-biphosphates, 2 Mg++s, and 97 HOHs #1fbd 2.9 tetramer (a4) - 2 chains given [335]; 2 2,5-anhydroglucitol- 1,6-biphosphates and 4 Mn++s #1fbe 3.0 tetramer (a4) - 2 chains given [335]; 2 2,5-anhydroglucitol- 1,6-biphosphates and 4 Zn++s #1fbf 2.7 tetramer (a4) - 2 chains given [335]; 2 2,5-anhydromannitol- 1,6-biphosphates, 2 Mg++s, and 44 HOHs #1fbg 3.0 tetramer (a4) - 2 chains given [335]; 2 2,5-anhydromannitol- 1,6-biphosphates and 2 Mn++s #1fbh 2.5 tetramer (a4) - 2 chains given [329, 330]; 2 FBPs and 110 HOHs #1fbp 2.5 tetramer (a4) - 2 chains given [335]; 2 F6Ps, 2 AMPs, and 2 Mgs #2fbp 2.8 tetramer (a4) - 2 chains given [335] #3fbp 2.8 tetramer (a4) - 2 chains given [335]; 2 F6Ps #4fbp 2.5 tetramer (a4) - 4 chains given [335]; 4 AMPs and 348 HOHs #5fbp 2.1 tetramer (a4) - 2 chains given [335]; 3 F6Ps and 308 HOHs #1fpb 2.6 tetramer (a4) - 2 chains given [335]; 3 FDPs #1frp 2.0 tetramer (a4) - 2 chains given [335]; 2 FDPs, 2 AMPs, 2 Zn++s, anc 239 HOHs Fructose-1,6-Bisphosphate Aldolase (Drosophila melanogaster, strain sevelen) (1fba.A: 1fba.A) {a/b singly wound para beta + anti beta + alpha cap + wedge alpha/coil} [barrel+] #1fba 1.9 tetramer (a4) - 4 chains given [361]; 1816 HOHs Fushi Tarazu Protein (Homeodomain) (Drosophila melanogaster) {a/a open face anti alpha cr + coil} XXX #1ftz NMR monomer? - 20 models given [70] D-Galactose/D-Glucose Binding Protein (Escherichia coli B/R) (2gbp: 1gca [2dri]) {domain 1: 1-110,258-293: a/b/a doubly wound para beta ud/ud} XXX Thornton dw3 {domain 2: 111-257,294-309: a/b/a doubly wound para beta ud/ud} [binding] #2gbp 1.9 monomer [309]; 1 beta-D-glucose, 1 Ca++, and 214 HOHs #1glg 2.0 monomer [309]; 1 GAL, 1 Ca++, and 215 HOHs Galactose Binding Protein (Salmonella typhimurium, strain lt2) (3gbp: 1gca [2dri]) {domain 1: 3-111,258-293: a/b/a doubly wound para beta ud/ud} {domain 2: 112-257,294-307: a/b/a doubly wound para beta ud/ud} [binding+] #3gbp 2.4 monomer [307]; supersedes 1gbp; 1 GLC, 1 Ca++, and 318 HOHs Galactose Oxidase (Dactylium dendroides) (1gof: 1gof) {domain 1: 1-153: double stranded beta cylinder + anti beta loop} {domain 2: 154-531: 7 X 4 anti beta wheel} {domain 3: 532-639: double stranded beta cylinder} #1gof 1.7 monomer? [639]; pH 4.5; 1 Cu++, 1 acetate, 1 Na+, and 316 HOHs; 2 SSs #1gog 1.9 monomer? [639]; pH 7.0; 1 Cu++, 1 Na+, and 310 HOHs; 2 SSs #1goh 2.2 monomer? [639]; apo; 1 Na+ and 310 HOHs; 2 SSs Gamma Delta Resolvase (Escherichia coli) (2rsl.C: 2rsl.C) {a/b/a doubly wound para beta ud/ud + anti beta + alpha} #2rsl 2.3 monomer - 3 chains given [140]; catalytic domain; supersedes 1rsl; 3 SO4s and 165 HOHs #1gdr 3.5 monomer [140]; catalytic domain GCN4 Leucine Zipper (Saccharomyces cerevisiae) (2zta.A: 2zta.A) {dimer: up down para alpha} #1dgc 3.0 dimer + dsDNA (a2 + d2) - 2 chains given [62, 19] #1ysa 2.9 dimer + dsDNA (ab + d2) - 4 chains given [57, 57, 20]; 17 HOHs #1zta NMR dimer (a2) - 20 models of 1 chain given [35] #2zta 1.8 dimer (a2) - 2 chains given [34]; 52 HOHs Gene 5 DNA Binding Protein (Filamentous bacteriophage FD, M13, and F1) (1bgh: 1bgh) {greek + loop anti beta} [gn5] #1bgh 1.8 dimer (a2) - 1 chain given [85]; 35 HOHs #2gn5 2.3 dimer (a2) - 1 chain given [87]; 12 HOHs #1gva NMR dimer (a2) - 20 models of 2 chains given [87]; Y41H mutant #1gvb NMR dimer (a2) - 1 model of 2 chains given [87]; minimized average structure; Y41H mutant GI Alpha 1 (Rattus rattus) {domain 1: 34-60, 179-343: a/b/a doubly wound para beta ud/ud} {domain 2: 61-178: Greek anti alpha} XXX or {domain 2: 61-178: partially encircled axial alpha} #1gia 2.0 monomer? [353]; 1 GSP, 1 Mg++, and 126 HOHs Glucagon (Sus scrofa) (1gcn: 1gcn) {alpha} #1gcn 3.0 trimer in crystal (a3) - 1 chain given [29]; monomer in solution; high temperature factors; presumed to be in crystalline config- uration on the receptor 1,3-1,4-Beta-Glucanase, Isoenzyme E2 (Hordeum vulgare) {a/b singly wound para beta + anti betas} [barrel+] #1ghr 2.2 monomer? [306]; 47 HOHs 1,3-Beta-Glucanase, Isozyme II (Hordeum vulgare) {a/b singly wound para beta + anti betas} [barrel+] #1ghs 2.2 monomer? [306]; 47 HOHs Hybrid 1-3,1-4-Beta-D-Glucan-4-Glucanohydrolase H(A16-M) (Bacillus amylolique- faciens and Bacillus macerans) (1ayh: 1ayh) {Greek anti beta} 6 loop #1ayh 2.0 monomer [214]; 1 Ca++ and 158 HOHs; 1 SS #1byh 2.8 monomer [214]; 1 butyl group, 2 GLCs, 1 Ca++, and 72 HOHs; 1 SS #1cpm 2.0 monomer [214]; circularly permuted; 1 Ca++ and 125 HOHs; 1 SS #1cpn 1.8 monomer [208]; circularly permuted; 1 Ca++ and 116 HOHs; 1 SS Glucoamylase (Aspergillus awamori, var. X100) (3gly: 3gly) {a/a singly wound para alpha + anti betas + alpha} *good for structure picture #1agm 2.4 monomer? [470]; 1 N-glycosyl chain (C32), 1 N-glycosyl chain (C52), 10 MANs, 2 acarboses, and 535 HOHs; 3 SSs #1dog 2.4 monomer? [470]; 1 NAG(A)-NAG(B)-GLC(C)-GLC(D)-GLC(G), 1 NAG(A)- NAG(B)-GLC(C)=GLC(D)-GLC(E)-GLC(F)-GLC(G)-GLC(H), 10 GLCs, 2 1-deoxynojirimycin, and 605 HOHs; 3 SSs #3gly 2.2 monomer? [470]; 4 NAGs, 19 MANs, and 673 HOHs; 3 SSs #1glm 2.4 monomer? [470]; 4 NAGs, 19 MANs, and 561 HOHs; 3 SSs Glucocorticoid Receptor (Rattus norvegicus) (1glu.A: 1glu.A [1hra]) {crossed alpha + anti betas + coil} #1glu 2.9 dimer + dsDNA (a2 + d2) - 4 chains given [81, 19]; fragment of protein (440 - 525); 4 Zn++s and 41 HOHs #1gdc NMR dimer (a2)? - 1 chain given [72]; minimized average structure protein (440 - 525); 2 Zn++s Glucose/Galactose Binding Protein (Salmonella typhimurium, strain LT2) (1gca: 1gca [2dri]) {domain 1: 1-111,258-293: a/b/a doubly wound para beta ud/ud} {domain 2: 112-257,294-309: a/b/a doubly wound para beta ud/ud + wedge alpha/coil} [binding+] #1gca 1.7 monomer? [309]; 1 GAL, 1 Ca++, and 153 HOHs #1gcg 1.9 monomer? [309]; closed, unliganded form; 1 Ca++, and 173 HOHs Glucose Oxidase (Aspergillus niger) (1gal: 1gal) {domain 1: 3-79,226-320,535-593: a/b/ab doubly wound para beta ud/udcr + alpha} XXX {domain 2: 980-225,321-534: a/b open face anti beta ud + anti beta loops + anti alpha loops} XXX #1gal 2.3 monomer? [583]; 1 FAD, 6 NAGs, 3 MANs, and 152 HOHs; 1 SS Glucose Permease (Bacillus subtilis) (1gpr: 1gpr [1f3g]) {greek + loop anti beta} #1gpr 1.9 monomer [162]; domain IIA; 100 HOHs D-Glucose 6-Phosphate Isomerase (Sus scrofa) (1pgi: ???) {domain 1: 1-275,421-514: a/b/a doubly wound para beta ud/ud + anti alpha} {domain 2: 276-420: a/b/a doubly wound para beta ud/ud} #1pgi 3.5 CA dimer (a2) - 1 chain given [514]; all residues UNK Glucokinase (Homo sapiens) {based on 2yhx} {domain 1: greek anti alpha + crossed alphas} {domain 2: a/b/a doubly wound anti beta ud/cr} {domain 3: a/b/a doubly wound mixed beta ud/cr} #1glk --- monomer? [465]; theoretical model; 1 GLC Beta-Glucosyltransferase (Bacteriophage T4) {domain 1: 1-161,338-351: a/b/a doubly wound para beta ud/ud} {domain 2: 162-337: a/b/a doubly wound para beta ud/ud} #1bgt 2.2 CA monomer? [351] #1bgu 2.2 CA monomer? [351]; 1 UDP Glutamine Phosphoribosylpyrophosphate Amidotransferase (Bacillus subtilis) {domain 1: 1-232: a/b/b/a back to back open face anti beta ud/ud} {domain 2: 233=465: a/b/a doubly wound para beta ud/ud + anti beta + alpha} #1gph 3.0 tetramer (a4) - 1 chain given [465]; 4 FS4s and 8 AMPs; Glutamine Synthase (Salmonella typhimurium) (2gls.A: 2gls.A) {domain 1: 1-100: multiple anti beta + alpha} {domain 2: 101-468: a/b open face anti beta ud + up down anti alpha + anti beta + alpha} [gls] #2gls 3.5 dodecamer (a12) - 12 chains given [469]; 24 Mn++s and 36 HOHs Glutaminyl-tRNA Synthetase (Escherichia coli) (1gsg.P: 1gsg.P) {domain 1: 8-102,211-260: a/b/a doubly wound para beta} {domain 2: 103-210: a/b/a doubly wound anti beta} {domain 3: 261-338: crossed alpha + alpha} {domain 4: 339-462: multiple anti beta} see s_prots {domain 5: 463-547: double stranded beta cylinder + anti alpha} #1gsg 2.8 CA monomer + substrate tRNA (a + s) - 2 chains given [553, 75] Glutaredoxin (Bacteriophage T4) (1aaz.A: 1aaz.A) {a/b/a doubly wound mixed beta ud/cr} #1aaz 2.0 monomer? - 2 chains given [87]; 2 Cds and 222 HOHs; 2 SSs #1aba 1.45 monomer [87]; V15G and Y16P mutant; 1 N-(ethylsulfite)-morpholine and 140 HOHs; 1 SS Glutaredoxin (Escherichia coli, strain n4830/PAHOB1) (1ego: 1ego) {a/b/a doubly wound mixed beta ud/cr} #1ego NMR monomer - 20 models given [85]; oxidized; 1 SS #1egr NMR monomer - 20 models given [85]; reduced #1grx NMR monomer - 20 models given [85]; C14S mutant; 1 glutathione Glutathione Peroxidase (Bos taurus) (1gp1.A: 1gp1.A) {a/b/ab doubly wound mixed beta ud/cr} [gp1] #1gp1 2.0 tetramer (a4) - 2 chains given [198]; 2 seleninic acids and 185 HOHs; difficult to make tetramer which looks correct Glutathione Reductase (Escherichia coli) {domain 1: 3-140,267-336: a/b/bc doubly wound para beta ud/cr + crossed alpha} {domain 2: 141-266: a/b/b doubly wound para beta ud/cr} {domain 3: 337-450: a/b open face anti beta ud + alpha} #1ger 1.86 dimer (a2) - 2 chains given [450]; 2 FADs and 645 HOHs #1ges 1.74 dimer (a2) - 2 chains given [450]; A179G, A183G, V197E, R198M, K199F, H200D, R204P mutant; 2 FADs and 585 HOHs #1get 2.00 dimer (a2) - 2 chains given [450]; 2 FADs, 2 NAPs, and 450 HOHs #1geu 2.2 dimer (a2) - 2 chains given [450]; A179G, A183G, V197E, R198M, K199F, H200D, R204P mutant; 2 FADs, 2 NADs and 410 HOHs Glutathione Reductase (Homo sapiens) (3grs: 3grs [1npx] [1lvl] [3lad.A] [2tpr.A]) {domain 1: 18-157,295-364: a/b/bc doubly wound para beta ud/cr + crossed alpha} {domain 2: 158-294: a/b/b doubly wound para beta ud/cr} {domain 3: 365-478: a/b open face anti beta ud + alpha} [fad_nadh] #1gra 2.0 dimer (a2) - 1 chain given [478]; oxidized; 1 FAD, 1 NADPH, 2 glutathiones, and 530 HOHs; 1 SS #1grb 1.85 dimer (a2) - 1 chain given [478]; oxidized; 1 FAD, 1 NAD, 1 phos- phate, 1 NADPH, and 527 HOHs #1gre 2.0 dimer (a2) - 1 chain given [478]; 1 FAD, 1 phosphate, 2 gluta- thiones, and 529 HOHs #1grf 2.0 dimer (a2) - 1 chain given [478]; 1 FAD, 1 phosphate, 1 carbox- amidomethyl, and 531 HOHs #1grg 2.0 dimer (a2) - 1 chain given [478]; 1 FAD, 1 phosphate, 1 chloro- ethylcarbamoyl, and 520 HOHs #1grh 3.0 dimer (a2) - 1 chain given [478]; 1 hydroxyethyl; coordinates for only Cys 58 and HETATM -- to be substituted into 1grg #3grs 1.54 dimer (a2) - 1 chain given [478]; oxidized; supersedes 2grs; 1 FAD, 1 phosphate, and 523 HOHs; 1 SS #4gr1 2.4 dimer (a2) - 1 chain given [478]; oxidized; inhibitor, retro- GSSG; 1 FAD, 1 phosphate, and 514 HOHs; 1 SS Glutathione S-Transferase (Schistosoma japonica) {domain 1: 1-80: a/b/a doubly wound mixed beta ud/cr} {domain 2: 81-232: a/a open face para alpha ud + wedge alpha} #1gne 2.5 monomer? [232]; fused with epitope form HIV1/GP41; 1 GSH and 126 HOHs Glutathione S-Transferase A1-1 (Homo sapiens) (1guh.A: 1guh.A [2gst.A] [1gsr.A]) {domain 1: 2-80,192-223: a/b/a doubly wound anti beta ud/cr} {domain 2: 81-191: a/a open face para alpha ud + crossed alpha} #1guh 2.6 dimer (a2) - 2 chains given [221]; 2 s-benzyl-glutathiones Glutathione S-Transferase, Class MU, GSTM2-2 (Homo sapiens) (1hna: 2gst.A [1guh.A] [1gsr.A]) {domain 1: 1-84,191-217: a/b/a doubly wound mixed beta ud/cr} {domain 2: 85-190: a/a open face para alpha ud} #1hna 1.85 dimer (a2) - 1 chain given [217]; form A; W214F mutant; 1 gluta- thione S-(2,4 dinitrobenzene) and 108 HOHs #1hnb 3.5 dimer (a2) - 2 chains given [217]; form B; W214F mutant; 2 gluta- thione S-(2,4 dinitrobenzene)s #1hnc 3.0 dimer (a2) - 4 chains given [217]; form C; W214F mutant; 4 gluta- thione S-(2,4 dinitrobenzene)s Glutathione S-Transferase, Class MU (Rattus rattus) (2gst.A: 2gst.A [1gsr.A] [1guh.A]) {domain 1: 1-84,191-217: a/b/a doubly wound mixed beta ud/cr} {domain 2: 85-190: a/a/open face para alpha ud} #1gsb 2.5 CA dimer? (a2) - 4 chains given [217]; isoenzyme 3-3; form B of crystal #1gsc 2.5 CA dimer? (a2) - 4 chains given [217]; isoenzyme 3-3; form C of crystal #1gst 2.2 dimer? (a2) - 2 chains given [217]; isoenzyme 3-3; 2 glutathiones and 474 HOHs #2gst 1.8 dimer? (a2) - 2 chains given [217]; isoenzyme 3-3; 2 (9S,10S)-9- (S-glutathioyl)-10-hydroxy-9,10-dihydrophenanthrenes, 2 SO4s, and 470 HOHs #3gst 1.9 dimer? (a2) - 2 chains given [217]; isoenzyme 3-3; 2 (9R,10R)-9- (S-glutathioyl)-10-hydroxy-9,10-dihydrophenanthrenes, 7 SO4s, and 437 HOHs #4gst 1.9 dimer? (a2) - 2 chains given [217]; isoenzyme 3-3; 2 1-(S- (glutathionyl)-2,4,6-trinitrocyclohexadienates, 6 SO4s, and 360 HOHs #5gst 2.0 dimer? (a2) - 2 chains given [217]; isoenzyme 3-3; 2 1-(S- (glutathionyl)-2,4-dinitrobenzenes, 1 SO4, and 332 HOHs Glutathione S-Transferase, Class PI (Homo sapiens) (1gss.A: 1gsr.A [2gst.A] [1guh.A]) {domain 1: 1-75,184-207: a/b/a doubly wound para beta ud/cr} {domain 2: 76-183: a/a open face para alpha ud} #1gss 2.8 dimer? (a2) + inhibitor - 4 chains given [209, 3]; 2 S-hexyl- cystines and 205 HOHs Glutathione S-Transferase YFYF, Class PI (Mus musculus) (1glp.A: {domain 1: 1-77,187-209: a/b open face mixed beta ud} {domain 2: 78-186: a/a open face para alpha ud + alpha wedge} #1glp 1.9 dimer? (a2) + inhibitor (2i) - 4 chains given [209], 1]; 2 GTSs and 182 HOHs #1glq 1.8 dimer? (a2) - 2 chains given [209], 1]; 2 GTBs and 148 HOHs Glutathione S-Transferase, Class PI (Sus scrofa) (1gsr.A: 1gsr.A [2gst.A] [1guh.A]) {domain 1: 1-75,185-209: a/b/a doubly wound para beta ud/cr} {domain 2: 76-184: a/a open face para alpha ud} #1gsr 2.3 dimer? (a2) - 2 chains given [207]; 2 glutathione SO4s Glutathione Synthase (Escherichia coli B) (1glt: 1glt) {domain 1: 1-122: a/b/a doubly wound para beta ud/ud + anti beta} {domain 2: 123-200: a/b open face anti beta ud + alpha} {domain 3: 201-316: a/b open face anti beta cr + wedge alpha} #1glt 2.0 monomer? [316]; 106 HOHs #1glv 2.7 monomer? [303]; loopless mutant (DEL226-241; INS(GGG)); 18 HOHs D-Glyceraldehyde-3-Phosphate Dehydrogenase (Bacillus stearothermophilus) (1gd1.O: 1gd1.O) {domain 1: 0-148,313-333: a/b/a doubly wound para beta + a/b open face anti beta} {domain 2: 149-312: a/b open face anti beta ud + a/b/c doubly wound para beta ud/ud} [nbd] #1gd1 1.8 tetramer (a4) - 4 chains given [334]; holo; 4 NADs, 8 SO4s, and 668 HOHs #2gd1 2.5 tetramer (a4) - 4 chains given [334]; apo; 8 SO4s and 504 HOHs D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homarus americanus) (4gpd.1: 1gd1.O) {domain 1: 1-147,316-333: a/b/a doubly wound para beta + a/b open face anti beta} {domain 2: 148-315: a/b open face anti beta ud + a/b/c doubly wound para beta ud/ud} [nbd] #1gpd 2.9 tetramer (a4) - 2 chains given [334]; 2 NADs and 4 phosphates #4gpd 2.8 tetramer (a4) - 4 chains given [333]; apo; supersedes 2gpd; 122 HOHs D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homo sapiens) (3gpd.G: 1gd1.O) {domain 1: 1-150,314-334: a/b/ac doubly wound para beta ud/ud + a/b open face anti beta ud} {domain 2: 151-313: a/b open face anti beta ud + a/b/c doubly wound para beta ud/ud} [nbd] #3gpd 3.5 tetramer (a4) - 2 chains given [334]; 2 NADs, 2 substrate phos- phates, 2 inorganic phosphates D-Glyceraldehyde-3-Phosphate Dehydrogenase (Trypanosoma brucei brucei) (1gga.O: 1gd1.O) {domain 1: 1-164,334-358: a/b/ac doubly wound para beta ud/ud + a/b open face anti beta ud} {domain 2: 164-333: a/b open face anti beta ud + a/b/c doubly wound para beta ud/ud} [nbd+] #1gga 3.2 tetramer (a4) - 6 chains given [358]; holo; use chains O, P, Q, and R for complete tetramer; 12 SO4s and 6 NADs D-Glycerate Dehydrogenase (Hyphomicrobium methylovorum) (1gdh.A: 1gdh.A) {domain 1: 2-101,290-322: a/b/a doubly wound para beta ud/ud} {domain 2: 102-289: a/b/a doubly wound para beta ud/ud + alpha + coil} #1gdh 2.4 dimer (a2) - 2 chains given [320]; 2 SO4s and 197 HOHs Glycerol Kinase (Escherichia coli) (1gla.G: 1gla.G) XXX check Cynthia {domain 1: 4-82,439-462: a/b doubly wound anti beta} {domain 2: 83-241: a/b doubly wound anti beta + 2 wedge alphas + 2 anti betas} {domain 3: 242-438,463-600: a/b doubly wound anti beta + a/b open face anti beta + alpha} or {domain 1: 4-82: a/b open face anti beta ud} {domain 2: 83-244: a/b/a doubly wound anti beta ud/ud + anti betas + wedge alphas} {domain 3: 245-600: a/b/a doubly wound anti beta ud/cr + a/b open face anti beta + alpha} #1gla 2.6 tetramer + factor III (a4 + 4b) - 2 chains given [501, 168]; 1 glycerol #1glb 2.6 tetramer + factor III (a4 + 4b) - 2 chains given [501, 168]; 1 glycerol and 1 ADP #1glc 2.65 tetramer + factor III (a4 + 4b) - 2 chains given [501, 168]; 1 G3P, 1 ADP, 1 Mg++, 1 Zn++, and 42 HOHs #1gld 2.93 tetramer + factor III (a4 + 4b) - 2 chains given [501, 168]; 1 G3P, 1 ADP, 1 Mn++, and 17 HOHs #1gle 2.94 tetramer + factor III (a4 + 4b) - 2 chains given [501, 168]; 1 G3P, 1 ADP, 2 Zn++s, and 48 HOHs Glycogen Phosphorylase (Oryctolagus cuniculus) (1gpb: 1gpb) XXX check structure again {domain 1: a/b/a doubly wound para beta + anti beta + misc alpha} {domain 2: a/b/a doubly wound para beta + anti beta + misc alpha} #1abb 2.8 tetramer (a4) - 4 chains given [828]; 4 pyridoxal diphosphates, 4 SO4s, and 4 inosine monophosphates #1gpa 2.9 tetramer (a4) - 4 chains given [842]; A: R state; 4 PLPs, 4 phos- phoryl groups bonded to S14, and 8 SO4s #1gpb 1.9 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP and 691 HOHs #2gpb 2.3 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 1 GLC, and 575 HOHs #3gpb 2.3 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 2 alpha- D-glucose-1-phosphates and 604 HOHs #4gpb 2.3 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 2 2- fluoro-2-deoxy-alpha-D-glucose-1-phosphates and 604 HOHs #5gpb 2.3 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 2 alpha- D- glucose-1-methylene-phosphates, 5 GLCs (from maltohexaose), and 595 HOHs #6gpb 2.86 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 1 heptu- lose 2-phosphate, 5 GLCs, 2 AMPs, and 608 HOHs #7gpb 2.9 tetramer (a4) - 4 chains given [842]; B: R state; 4 PLPs, 7 sul- fates, and 4 AMPs #8gpb 2.2 tetramer (a4) - 1 chain given [842]; B: T state; 1 PLP, 2 AMPs, and 640 HOHs #9gpb 2.9 tetramer (a4) - 4 chains given [842]; B: R state; 4 PLPs and 12 SO4s #1gpy 2.4 tetramer (a4) - 1 chain given [842]; B: T state; 1 alpha-D- glucose-6-phosphate, 1 PLP, and 673 HOHs #1pyg 2.87 tetramer (a4) - 4 chains given [842]; B; 4 AMPs and 4 PLPs Glycolate Oxidase (Spinacia oleracea) (1gox: 1gox [1fcb.A.2]) {a/b singly wound para beta + anti beta cap + anti beta + anti alphas} [barrel] #1gox 2.0 octamer (a8) or tetramer (a4) (in equilibrium) - 1 chain given [369]; 1 FMN and 298 HOHs Gramicidin A (Bacillus brevis) (1gma.A: 1gma.A) {anti beta double helix} (1grm: 1gma.A) {para beta cylinder} #1gma 0.86 dimer (a2) - 2 chains given [17]; several amino acids are in D config; 2 ethanolamines, 14 ethanols, and 2 HOHs; membrane protein #1grm NMR dimer (a2) - 5 models of 2 chains given [17]; several amino acids are in D config; 2 ethanolamines; membrane protein Granulocyte Colony Stimulating Factor (Bos taurus) (1bgc: 1bgc) {up down anti alpha + crossed alpha} #1bgc 1.7 monomer? [174]; 97 HOHs; 2 SSs Granulocyte Colony Stimulating Factor (Canis familiaris) (1bgd: 1bgc) {up down anti alpha + crossed alpha} #1bgd 2.3 monomer? [175]; form I; 58 HOHs; 2 SSs #1bge 2.2 monomer? - 2 chains given [175]; form II; 133 HOHs; 4 SSs Granulocyte Colony Stimulating Factor (Homo sapiens) (1rhg.A: 1bgc) {up down anti alpha + crossed alpha} #1rhg 2.2 monomer? - 3 chains given [174]; 6 SSs #1gnc NMR monomer? - 10 models [178]; 2 SSs Granulocyte-Macrophage Colony-Stimulating Factor (Escherichia coli and Homo sapiens) (1gmf.A: 1gmf.A) {up down anti alpha + anti beta} alpha pair, beta pair alpha pair spiral #1csg 2.7 monomer? - 2 chains given [127]; 4 SSs #1gmf 2.4 monomer - 2 chains given [127]; 4 SSs Growth Factor Receptor-Bound Protein 2 (Homo sapiens) {Greek anti beta} #1gfc NMR monomer? [59]; minimized average structure #1gfd NMR monomer - 20 models given [59] Growth Hormone (Homo sapiens) (1huw: 1huw) {up down anti alpha + anti beta} alpha pair, beta pair alpha pair spiral #2hhr 2.8 CA monomer + receptor domain (a + 2b) - 3 chains given [190, 203] #1huw 2.0 monomer [166]; F10A, M14W, H18D, H21N, K41I, Y42H, L45W, Q46W, F54P, R64K, R167N, D171S, E174S, F176Y, I179T mutant; 77 HOHs; 2 SSs Growth Hormone Receptor (Homo sapiens) (2hhr.B: 2hhr.B) {domain 1: 32-128: Greek anti beta} 3loop duodudud {domain 2: 129-236: Greek anti beta} DUP2hhr 2.8 CA 2 monomers + ligand (2b + a) - 3 chains given [203, 190] Guanylate Kinase (Saccharomyces cerevisiae) (1gky: 1gky) {a/b/a doubly wound para beta ud/ud + a/b/c doubly wound para beta ud/ud + anti beta pair} #1gky 2.0 monomer [186]; 1 guanosine 5 monophosphate, 1 SO4, and 173 HOHs Guanylin (Homo sapiens) {SS-rich coil} #1gna NMR monomer - 20 models given [13]; A-form; 2 SSs #1gnb NMR monomer - 20 models given [13]; B-form; 2 SSs Haloalkane Dehalogenase (Xanthobacter autotrophicus, strain GJ10) (2had: 2had) {a/b/a doubly wound para beta ud/ud + anti alpha pairs} #2eda 2.19 monomer? [310]; 1 iodide and 214 HOHs #1edb 2.01 monomer? [310]; pH 6.2; 1 Cl- and 191 HOHs #2edc 2.3 monomer? [310]; 1 I- and 125 HOHs #1edd 2.10 monomer? [310]; pH 8; 1 Cl- and 172 HOHs #1ede 1.9 monomer? [310]; pH 8.2; 204 HOHs #2had 1.9 monomer? [310]; pH 6.2; 258 HOHs Hannuka Factor (Homo sapiens) (1hf1: 1hf1 [2cga.A] [3est] [1tgn] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: Greek anti beta} {domain 2: Greek anti beta} [s_prot+] #1hf1 --- monomer? - 1 chain [234]; model Heat-Labile Enterotoxin (Escherichia coli) (1lts.A: 1lts.A) {alpha + coil} (1lts.C: 1lts.C) {a/b open face anti beta ud + a/b open face anti beta ud + crossed alpha} (1lts.D: 1lts.D) {domain 1: a/b open face anti beta} XXX look again {domain 2: a/b open face anti beta} or {Greek anti beta + alpha} 3 loop #1lta 2.2 hexamer (a, cleaved + b5) - 7 chains given [188, 45, 103]; 5 D- galactoses and 295 HOHs; 6 SSs #1ltb 2.2 hexamer (a, cleaved + b5) - 7 chains given [188, 45, 103]; par- tially activated by trypsin cleavage; 197 HOHs; 6 SSs #1lts 1.95 hexamer (a, cleaved + b5) - 7 chains given [185, 41, 103]; 293 HOHs; 6 SSs #1ltt 2.3 hexamer (a, cleaved + b5) - 7 chains given [185, 41, 103]; 5 lactoses, 5 GLCs, and 334 HOHs; 6 SSs Heat Shock Cognate Protein (Bos taurus) (1atr: 1atr) {domain 1: 2-38,116-174,361-384: a/b/a doubly wound para beta ud/ud + anti beta} {domain 2: 39-115: a/b open face anti beta cr + a/b open face anti beta ud} {domain 3: 175-230,299-360: a/b/a doubly wound para beta ud/cr} {domain 4: 231-298: a/b open face anti beta ud + crossed alpha} #1atr 2.34 monomer [386]; N-terminal fragment; T204V mutant; 1 ADP, 1 Mg++, 1 phosphate, and 116 HOHs #1ats 2.43 monomer [386]; N-terminal fragment; T204E mutant; 1 ADP, 1 Mg++, 1 phosphate, and 118 HOHs #1hsc 2.2 CA monomer [385]; N-terminal fragment Hemagglutinin (Influenza virus, 1968 X.31 strain) bromelain digested (missing hydrophobic anchor) (1hgf.A: 1hgf.A) [hmg-1] (1hgf.B: 1hgf.B) [hmg-2] {domain 1: A:1-18,B:1-75: a/b open face anti beta ud + up down anti alphas} {domain 2: A:19-115,A:260-328: a/b/b doubly wound para beta ud/cr + anti beta pairs} {domain 3: A:116-259: double stranded beta cylinder + anti beta loop} #1hgd 2.7 trimer of dimers (3[ab]) - 6 chains given [328, 175]; HA1:G135R mutant; 18 NAGs, 3 MANs, and 72 HOHs; 18 SSs #1hge 2.6 trimer of dimers (3[ab]) - 6 chains given [328, 175]; HA1:G135R mutant; 1 alpha-2-O-methyl-5-N-acetyl-neuraminic acid, 18 NAGs, 3 MANs, and 72 HOHs; 18 SSs #1hgf 2.6 trimer of dimers (3[ab]) - 6 chains given [328, 175]; bromelain digested; 18 NAGs and 3 MANs; 18 SSs #1hgg 2.9 trimer of dimers (3[ab]) - 6 chains given [328, 175]; bromelain digested; 18 NAGs, 3 MANs, 6 5-N-acetyl-alpha-D-neuraminic acids, 6 GALs, 6 GLCs, and 72 HOHs; 18 SSs #1hgh 2.7 trimer of dimers (3[ab]) - 6 chains given [328, 175]; 6 alpha- 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acids, 18 NAGs, 3 alpha- D- mannoses and 72 HOHs; 18 SSs #1hgi 2.7 trimer of dimers (3[ab]) - 6 chains given [328, 175]; 3 alpha- 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acids, 18 NAGs, 3 alpha- D-mannoses, and 72 HOHs; 18 SSs #1hgj 2.7 trimer of dimers (3[ab]) - 6 chains given [328, 175]; 3 9-amino- 9-deoxy-alpha-2-O-methyl-5-N-acetyl-neuraminic acids, 18 NAGs, 3 MANs, and 72 HOHs; 18 SSs DUP1him 2.9 HA1 fragment + antibody dimer (a + LH) - 6 chains given [8, 217, 220]; 2 terminal amides DUP1hin 3.1 HA1 fragment + antibody dimer (a + LH) - 3 chains given [8, 217, 220]; 22 HOHs #2hmg 3.0 trimer of dimers (3[ab]) - 6 chains given [328, 175]; HA1:G146D mutant; supersedes 1hmg; 18 NAGs, 3 MANs, and 33 HOHs; 18 SSs #3hmg 2.9 trimer of dimers (3[ab]) - 6 chains given [328, 175]; L226Q mutant; 18 NAGs, 3 MANs, and 33 HOHs; 18 SSs #4hmg 3.0 trimer of dimers (3[ab]) - 6 chains given [328, 175]; L226Q mutant; 18 NAGs, 3 MANs, 3 sialic acids, and 33 HOHs; 18 SSs #5hmg 3.2 trimer of dimers (3[ab]) - 6 chains given [328, 175]; HA2:D112G mutant; 18 NAGs, 3 MANs, 3 sialic acids, and 33 HOHs; 18 SSs DUP1ifh 2.8 HA1 fragment + antibody dimer (a + LH) - 3 chains given [8, 218, 220]; 1 HOH; 4 SSs Hemagglutinin (Influenza virus, X.47 strain) {coil} DUP1frg 2.8 peptide + dimer (p + ab) - 2 chains given [10, 217, 220]; 1 NH2 and 1 HOH; 3 SSs Hemerythrin (Siphonosoma species) (1hr3.A: ???) {up down anti alpha} [hmr?] #1hr3 5.5 CA trimer (a3) - 3 chains given [118]; all residues UNK; 3 mono- azido-mu-oxo-diirons Hemerythrin (Themiste dyscritum) (2hmq.A: 2hmq.A [2mhr]) {up down anti alpha} [hmr] #1hmd 2.0 octamer (a8) - 4 chains given [113]; two chains each from two different octamers; deoxy; S64 is acetylated; 4 mu-oxo-diirons and 293 HOHs #1hmo 2.0 octamer (a8) - 4 chains given [113]; two chains each from two different octamers; oxy; S64 is acetylated; 4 dioxygens, 4 mu- oxo-diirons and 293 HOHs #2hmq 1.66 octamer (a8) - 4 chains given [113]; supersedes 1hmq; two chains each from two different octamers; A64 acetylated; met; residue 21 modeled both as V and I; 4 mu-oxo-diirons, 4 acetato groups, and 293 HOHs #2hmz 1.66 octamer (a8) - 4 chains given [113]; supersedes 1hmz; two chains each from two different octamers; A64 acetylated; azidomet; residue 21 modeled both as V and I; 4 monoazido-mu-oxo-diirons, 4 acetato groups and 282 HOHs Hemerythrin B (Phascolopsis gouldii) (1hrb: 2hmq.A [2mhr]) {up down anti alpha} #1hrb 5.5 CA monomer [113]; 2 Fe+++s Hemocyanin (Limulus polyphemus) (1lla: 1lla [1hcy]) {domain 1: 2-119, 166-192, 513-541: up down anti alpha + crossed alpha} {domain 2: 193-377: up down anti alpha + anti beta} {domain 3: 378-404, 442-512, 542-628: Greek anti beta} {domain 4: 120-165, 405-441: anti beta + alpha} or XXX {domain 1: 2-108: a/a open face para alpha ud} XXX {domain 2: 109-377: up down anti alpha pairs + anti beta} {domain 3: 378-628: Greek anti beta + alpha} #1lla 2.2 monomer? [628]; subunit type II; 2 Cu+s, 1 Na+, 1 Cl-, and 332 HOHs; 2 SSs Hemocyanin (Panuliris interruptus) (1hcy: 1hcy [1lla]) XXX Cynthia check {domain 1: 1-145: a/a/a doubly wound para alpha ud/cr} *good for picture {domain 2: 146-170,423-458: a/b open face anti beta ud} {domain 3: 171-397: up down anti alphas + anti beta} {domain 4: 398-422,459-653: Greek anti beta + alphas} #1hc1 3.2 hexamer (a6) - 1 chain given [657]; subunit 1; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hc2 3.2 hexamer (a6) - 1 chain given [657]; subunit 2; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hc3 3.2 hexamer (a6) - 1 chain given [657]; subunit 3; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hc4 3.2 hexamer (a6) - 1 chain given [657]; subunit 4; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hc5 3.2 hexamer (a6) - 1 chain given [657]; subunit 5; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hc6 3.2 hexamer (a6) - 1 chain given [657]; subunit 6; deoxygenated; 2 Cu+s and 186 HOHs; full hexamer can be generated by combining 1hc1-1hc6; 3 SSs #1hcy 3.2 hexamer (a6) - 1 chain given [657]; deoxygenated, symmetrized; 2 NAGs, 2 Cu+s, and 186 HOHs; 3 SSs Hemoglobin (Equus caballus) (2mhb.A: 2hhb.A [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] (2mhb.B: 2hhb.B [2hhb.A] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] #2dhb 2.8 tetramer (a2b2) - 2 chains given [141, 146]; deoxy; supersedes 1dhb; 2 HEMs with Fe++ and 2 HOHs; chain A: res 63, 65 are A, G vs. G, A in 2mhb; chain B: res 111 - 114 ALVV vs. VVVL in 2mhb #2mhb 2.0 tetramer (a2b2) - 2 chains given [141, 146]; supersedes 1mhb; aquo met; 2 HEMs with Fe+++ and 2 HOHs Hemoglobin (Glycera dibranchiata) (2hbg: 2hbg [2hhb.A] [2hhb.B] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #1hbg 1.5 monomer [147]; 1 HEM with Fe++ and CO and 155 HOHs #2hbg 1.5 monomer [147]; 1 HEM with Fe++ and 146 HOHs Hemoglobin (Homo sapiens) (2hhb.A: 2hhb.A [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] (2hhb.B: 2hhb.B [2hhb.A] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] #1bab 1.5 tetramer (a2b2) - 4 chains given [143, 146]; A chain: V1E + acetylated 0 Met variant (Thionville); 4 HEMs with Fe++, 2 sul- fates, and 266 HOHs #1bbb 1.7 tetramer (a2b2) - 4 chains given [141, 146]; A form; carbon- monoxy; 4 HEMs with Fe++, 4 COs, and 302 HOHs #1cbl 1.9 tetramer (b4) - 4 chains given [146]; beta chain only tetramer; "R-like" form; 4 HEMs with Fe++, 4 SO4s, and 71 HOHs #1cbm 1.8 tetramer (b4) - 4 chains given [146]; beta chain only tetramer; carbonmonoxy; "R-like" form; 4 HEMs with Fe++, 4 COs, 4 SO4s, and 133 HOHs #1cmy 3.0 tetramer (a2b2) - 4 chains given [141, 146]; Ypsilanti; carbon- monoxy; 4 HEMs with Fe++ #1coh 2.9 tetramer (a2b2) - 4 chains given [141, 146]; T state; 2 HEMs with Co++, 2 HEMs with Fe++ and CO, and 200 HOHs #1dxt 1.8 tetramer (a2b2) - 4 chains given [141, 147]; recombinant B chain with N-terminal Met; 4 HEMs with Fe++ and 227 HOH #1dxu 1.8 tetramer (a2b2) - 4 chains given [141, 147]; recombinant B chain with V1M mutation; 4 HEMs with Fe++, 2 SO4s, and 235 HOHs #1dxv 1.8 tetramer (a2b2) - 4 chains given [141, 147]; recombinant B chain with V1A mutation; 4 HEMs with Fe++, 2 SO4s, and 232 HOHs #1hba 2.1 tetramer (a2b2) - 4 chains given [141, 146]; Rothschild variant, B:W37R; deoxy; 4 HEMs with Fe++, 2 Cl-s, and 201 HOHs #1hbb 1.9 tetramer (a2b2) - 4 chains given [141, 146]; deoxy, low salt, 100 mm Cl; 4 HEMs with Fe++ and 192 HOHs #1hbs 3.0 tetramer (a2b2) - 8 chains given [141, 146]; deoxy; chain 2: E6V mutant = sickle cell; 8 HEMs with Fe++ #1hco 2.7 tetramer (a2b2) - 2 chains given [141, 146]; carbonmonoxy; not energy minimized; 2 HEMs with Fe++ #2hco 2.7 tetramer (a2b2) - 2 chains given [141, 146]; carbonmonoxy; energy minimized; 2 HEMs with Fe++ #1hga 2.1 tetramer (a2b2) - 4 chains given [141, 146]; T state, deoxygen- ated; 4 HEMs with Fe++ and 89 HOHs #1hgb 2.1 tetramer (a2b2) - 4 chains given [141, 146]; T state, aquomet; 4 HEMs with Fe++, 4 ligand HOHs, and 202 HOHs #1hgc 2.1 tetramer (a2b2) - 4 chains given [141, 146]; T state, aquomet; 4 HEMs with Fe++, 2 ligand O2s, and 89 HOHs #2hhb 1.74 tetramer (a2b2) - 4 chains given [141, 146]; deoxy; supersedes 1hhb; "best estimate of coordinates"; 4 HEMs with Fe++, 2 phos- phates, and 221 HOHs #3hhb 1.74 tetramer (a2b2) - 2 chains given [141, 146]; deoxy; supersedes 1hhb; "symmetry averaged"; 2 HEMs with Fe++, 1 phosphate, and 54 HOHs #4hhb 1.74 tetramer (a2b2) - 4 chains given [141, 146]; deoxy; supersedes 1hhb; "unrestrained refinement"; 4 HEMs with Fe++, 2 phosphates, and 223 HOHs #1hho 2.1 tetramer (a2b2) - 2 chains given [141, 146]; A; oxy; 2 HEMs with Fe++, 1 phosphate, and 109 HOHs #1nih 2.6 tetramer (a2b2) - 4 chains given [141, 146]; T state; 2 alpha- chain HEMs with Ni(II), 2 beta-chain HEMs with Fe++ and CO, 1 inositol hexaphosphate, and 52 HOHs #1thb 1.5 tetramer (a2b2) - 4 chains given [141, 146]; T state; partially oxygenated; 4 HEMs with Fe++, 1 inositol hexaphosphate, and 314 HOHs Hemoglobin F (Fetal) (Homo sapiens) (1fdh.A: see 2hhb.A) (1fdh.G: 2hhb.B [2hhb.A] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] #1fdh 2.5 tetramer (a2b2) - 2 chains given [141, 147]; deoxy; 2 HEMs with Fe Hemoglobin I (Lucina pectinata) {heme binding Greek anti alpha} #1flp 1.5 monomer [142]; 1 HEM with Fe++ and 131 HOHs Hemoglobin I (Scapharca inaequivalvis archid) {heme binding Greek anti alpha} #1hbi 1.7 dimer (a2) - 2 chains given [146]; 2 HEMs with Fe++, 1 O2, and 218 HOHs Hemoglobin S (Sickle Cell) (Odocoileus virginianus) (1hds.A: 2hhb.A [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] (1hds.B: 2hhb.B [2hhb.A] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #1hds 1.98 tetramer (a2b2) - 4 chains given [141, 145]; 4 HEMs with Fe Hemoglobin (Pagothenia bernacchii) (1pbx.A: 2hhb.A [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] (1pbx.B: 1pbx.B [2hhb.A] [2hhb.B] [2hbg] [3sdh.A] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #1pbx 2.5 tetramer(a2b2) - 2 chains given [142, 146]; carbonmonoxy; 2 HEMs with Fe and CO and 28 HOHs Hemoglobin (Scapharca inaequivalvis) (3sdh.A: 3sdh.A [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [1mbd] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #3sdh 1.4 dimer (a2) - 2 chains given [146]; supersedes 1sdh; carbonmonoxy; 2 HEMs with Fe++ and CO and 265 HOHs #4sdh 1.6 dimer (a2) - 2 chains given [146]; supersedes 2sdh; deoxy; 2 HEMs with Fe++ and 219 HOHs Hemoglobin (Urechis caupo) (1ith.A: 1ith.A) {heme binding Greek anti alpha} [globin+] #1ith 2.5 tetramer (a4) - 2 chains given [142]; 2 HEMs with Fe++ and 150 HOHs Hemoglobin III (Erythrocruorin) (Chironomous Thummi Thummi) (1ecd: 1ecd) {heme binding Greek anti alpha} [globin] #1eca 1.4 monomer [136]; aquo met; 1 HEM with Fe+++ and H2O and 94 HOHs #1ecd 1.4 monomer [136]; deoxy; 1 HEM with Fe++ and H2O and 94 HOHs #1ecn 1.4 monomer [136]; cyano met; 1 HEM with Fe+++ and CN and 94 HOHs #1eco 1.4 monomer [136]; carbon monoxy; 1 HEM with Fe++ and CO and 94 HOHs Hemoglobin V (Petromyzon marinus) (2lhb: 2lhb [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [1mba]) {heme binding Greek anti alpha} [globin] #2lhb 2.0 monomer or dimer (a1 or a2) - 1 chain given [149]; cyano, met; Hs added by computer; 1 HEM with Fe+++ and CN and 215 HOHs Hevein (Hevea brasiliensis) (1hev: 1hev [9wga.A]) {SS rich a/b/c doubly wound anti beta cr/ud} #1hev NMR monomer - 6 models given [43]; 4 SSs Hexokinase A (Saccharomyces cerevisiae) (1hkg: 2yhx) {domain 1: 2-18,247-363: greek anti alpha + crossed alphas} {domain 2: 19-46,189-246,364-431: a/b/a doubly wound anti beta ud/cr} {domain 3: 47-188,432-458: a/b/a doubly wound mixed beta ud/cr} #1hkg 3.5 monomer [457]; complex with GLC; many UNK residues Hexokinase B (Saccharomyces cerevisiae) (2yhx: 2yhx) {domain 1: 2-18,247-371: greek anti alpha + crossed alphas} {domain 2: 19-57,189-246,372-431: a/b/a doubly wound anti beta ud/cr} {domain 3: 58-188,432-457: a/b/a doubly wound mixed beta ud/cr} #2yhx 2.1 probably multimer - 1 chain given [457]; supersedes 1yhx; 1 orthotoluoylglucosamine; many residues UNK HHAI DNA (Cytosine-C5-)-Methyltransferase (Haemophilus haemolyticus) (1hmy: 1hmy) {domain 1: 1-195, 308-328: a/b/a doubly wound mixed beta ud/ud} {domain 2: 189-272: open face anti beta + anti beta} {domain 3: 273-307: c/a open face para alpha cr} #1hmy 2.5 monomer? [327]; 1 S-adenosylmethionine High Potential Iron Protein (HIPIP) (Chromatium vinosum, strain D) (1hip: 1hip) {metal rich open face anti betas + alpha + coil} [hip] #1hip 2.0 monomer [85]; 1 FS4 cluster and 144 HOHs High Potential Iron Protein (HIPIP) (Ectothiorhodospira halophila) (2hip.A: 2hip.A) {metal rich open face anti betas + coil} [hip+] 3 layers: ac ab ab #2hip 2.5 monomer - 2 chains given [72]; 2 FS4 clusters and 104 HOHs High Potential Iron Protein (HIPIP) (Rhodocyclus tenuis) (1isu.A: 1isu.A) {metal rich open face anti betas + alpha + coil} [hip+] 2 layers ab ab #1isu 1.5 monomer? - 2 chains given [62]; 2 FS4 clusters and 143 HOHs Hirudin (Hirudo medicinalis) (5hir: 5hir) {SS rich anti beta} 2 loop DUP1dwb 3.18 fragment + alpha-thrombin (f + ab) [11, 36, 259]; 1 benzamidine and 50 HOHs; 4 SSs DUP1dwc 3.0 fragment + alpha-thrombin (f + ab) [11, 36n 259]; 1 MD-805 and 50 HOHs; 4 SSs DUP1dwd 3.0 fragment + alpha-thrombin (f + ab) [11, 36, 259]; 1 N==alpha== -(2-naphthyl-sulfonyl-glycyyl)-(DL)-para-amidinophenylalanyl- piperidine and 50 HOHs; 4 SSs DUP1dwe 3.0 fragment + alpha-thrombin + peptide (f + ab + p) [11, 36, 259, 4]; 1 D-Phe-Pro-Arg-chloromethylketone, 1 methylene, and 55 HOHs; 4 SSs DUP1fph 2.5 fragment + thrombin + fibrinopeptide - 4 chains given [12, 36, 259, 12]; 1 methylene and 168 HOHs; 4 SSs #1hic NMR monomer - 20 models given [51]; variant 1; residues 1 - 51 only; 3 SSs #2hir NMR monomer - 32 models given [65]; wt; 3 SSs #4hir NMR monomer - 32 models given [65]; K47E mutant; 3 SSs #5hir NMR monomer [65]; energy-minimized average structure; 3 SSs #6hir NMR monomer [65]; K47E mutant; minimized average structure; 2 SSs DUP1hrt 2.8 monomer + thrombin (cleaved, LH) - 3 chains given [65, 49, 259]; variant 1; 129 HOHs DUP3htc 2.3 CA hirudin variant 2 + thrombin (cleaved, LH) - 3 chains given [65, 259, 36]; variant 2, K47; 7 SSs DUP4htc 2.3 hirudin variant 2 I thrombin (cleaved, LH) - 3 chains given [65, 259, 36]; hirudin: variant 2, K47; 1 NAG and 262 HOHs; 7 SSs Hirulog 3 (Homo sapiens?) (1abi.I: 5hir) {coil} DUP1abi 2.3 monomer + alpha-thrombin (cleaved, LH) [20, 36, 259]; 1 beta- homoarginine, 1 D-phenylalanine, and 246 HOHs; 4 SSs Hisactophilin (Dityostellium discoideum) {6 anti beta pairs on cube faces} #1hcd NMR monomer [118] #1hce NMR monomer [118]; minimized average structure Histidine-Containing Phosphocarrier Protein (Bacillus subtilis) (2hpr: 1ptf [1poh]) {a/b open face anti beta ud} {two-stranded cylinder wrap} #1hid NMR monomer? [87]; minimized average structure #1hdn NMR monomer? - 30 models given [85] #2hpr 2.0 monomer? [87]; M51V and S83C mutant; 1 O bound to Cys 83, 1 sul- fate, and 89 HOHs Histidine-Containing Phosphocarrier Protein (Streptococcus faecalis, Strain HPR) (1ptf: 1ptf [1poh]) {a/b open face anti beta ud} #1ptf 1.6 monomer [88]; 99 HOHs Histone H1, Varians 11L (Gallus gallus) {crossed alpha bundle 3 + anti beta} #1ghc NMR monomer - 14 models given [75]; globular domain Histone H5 (Gallus gallus) (1hst.A: 1hst.A) {crossed alpha bundle 3 + open face anti beta} #1hst 2.6 monomer - 2 chains given [90]; globular domain Human Class I Histocompatibility Antigen A2/A2.1 (Homo sapiens) (3hla.A: 1hsb.A) {domain 1: 1-181: a/b open face anti beta cr} [hla_a2] {domain 2: 182-270: Greek anti beta} [igb] 3 loop #1hla 3.5 CA monomer + beta-2-microglobulin antigen (a + b) - 2 chains given [270, 97]; A2; 3 SSs #3hla 2.6 monomer + beta-2-microglobulin antigen (a + b) - 2 chains given [270, 99]; 46 HOHs; A2.1; 2 additional residues at C terminus of B chain; 3 SSs Human Class I Histocompatibility Antigen A 0201 (Homo sapiens) (1hhi.A: 1hsb.A) {domain 1: 1-180: a/b open face anti beta cr} [hla_a2+] {domain 2: 181-275: Greek anti beta} [igb+] 3 loop #1hhg 2.6 monomer + beta-2-microglobulin + HIV-1 envelop peptide - 6 chains given [275, 100, 9]; heavy chain of HLA; residues 195-207 of HIV-1 GP120; 6 SSs #1hhh 3.0 monomer + beta-2-microglobulin + hepatitis B nucleocapsid pep- tide - 3 chains given [275, 100, 10]; heavy chain of HLA; 3 SSs #1hhi 2.5 monomer + beta-2-microglobulin + influenza A protein frament - 6 chains given [275, 100, 9]; heavy chain of HLA; residues 58-66 of influenza A matrix protein M1; 6 SSs #1hhj 2.5 monomer + beta-2-microglobulin + HIV-1 reverse transcriptase peptide - 6 chains given [275, 100, 9]; heavy chain of HLA; residues 309-317 of HIV-1 reverse transcriptase; 6 SSs #1hhk 2.5 monomer + beta-2-microglobulin + HTLV-1 tax protein peptide - 6 chains given [275, 100, 9]; heavy chain of HLA; residues 11-19 of HTLV-1 tax protein; 6 SSs Human Class I Histocompatibility Antigen AW 68.1 (Homo sapiens) membrane anchor cleaved off with papain (1hsb.A: 1hsb.A) {domain 1: 1-181: a/b open face anti beta cr} [hla_a2+] {domain 2: 182-270: Greek anti beta} [igb+] #2hla 2.6 monomer + beta-2-microglobulin antigen (a + b) - 2 chains given [270, 99]; 10 HOHs; 3 SSs #1hsb 1.9 monomer + beta-2-microglobulin antigen (a + b + 2 peptides) - 4 chains given [270, 99, 3, 2]; 270 HOHs; 3 SSs Human Class I Histocompatibility Antigen B*2705 (Homo sapiens) (1hsa.A: 1hsb.A) {domain 1: 1-181: a/b open face anti beta cr} {domain 2: 182-276: Greek anti beta} #1hsa 2.1 monomer + beta-2-microglobulin antigen + peptide (a + b + c) - 6 chains given [276, 99, 9]; 440 HOHs; 6 SSs MHC Class I Histocompatibility Antigen H-2K(B) (Mus musculus) (1vaa.A: 1hsb.A) {domain 1: 1-180: a/b open face anti beta cr} {domain 2: 181-274: Greek anti beta} #2mha 2.8 dimer (LH) + peptide - 6 chains given [270, 99, 8]; A chain: 4 fewer residues at C terminus; 2mha.B is same as 1vaa.B #1vaa 2.3 monomer + microglobulin + VSV peptide - 3 chains given [274, 99, 8]; 114 HOHs; 3 SSs #1vab 2.5 monomer + microglobulin + Sendai virus peptide - 3 chains given [274, 99, 9]; 91 HOHs; 3 SSs Human Class II Histocompatibility Protein HLA-DR1 (Homo sapiens) {domain 1: A:3-A:81,B:3-B:92: a/b open face anti beta cr} {domain 2: A:82-A182: Greek anti beta} {domain 3: B:93-B:190: Greek anti beta} #1dlh 2.8 tetramer + peptide (2ab + 2p) - 6 chains given [180, 188, 13]; 8 NAGs and 153 HOHs; 6 SSs Human Chorionic Gonadotropin (Homo sapiens) {anti beta loops XXX} #1hcn 2.6 dimer? (ab) - 2 chains given [92, 145]; 2 NAGs and 63 HOHs; 11 SSs HIN Recombinase (Synthetic) {a/a open face anti alpha cr} #1hcr 1.8 monomer + dsDNA (a + cd) - 3 chains given [52, 14, 13]; 16 HOHs XXXXXXXXXXXXXXXXX HIV-1 GP120 Protein (HIV I, strain MN) (1ggi.P: 1ggi.P) {coil} DUP1ggi 2.8 fragment + antibody (f + ab) - 6 chains given [16, 218, 222]; residues 311-328 DUP1acy 3.0 fragment + antibody (f + ab) - 3 chains given [24, 215, 221]; 5 SSs; residues 308-332 HIV-1 P7 Nucleocapsid Protein (HIV I, strain MN) (1aaf: 1aaf [2znf]) {metal rich coil} #1aaf NMR monomer - 20 models given [55]; 2 Zn++s #1hvn NMR fragment + ssDNA - 15 models given [18, 5]; 5'-ACGCC-3'; with hbond constraints to GUA base; E:I1V and E:K14R vs 1aaf; 1 Zn++ #1hvo NMR fragment + ssDNA - 15 models given [18, 5]; 5'-ACGCC-3'; without hbond constraints to GUA base; E:I1V and E:K14R vs 1aaf; 1 Zn++ #1ncp NMR monomer - 2 models with 1 domain each given [17, 18]; minimized average structure; C:R1K vs. 1aaf; N:I1V, I12T, K14r vs 1aaf; 2 Zn++; 3 SSs #2znf NMR monomer - 16 models given [18]; I1V and K14R vs 1aaf; 1 Zn HIV-1 Protease (HIV I) (5hvp.A: 5hvp.A [2mip.A]) {Greek anti beta + anti beta + alpha} [virus_prot] 3 layer 3 loop BRU isolate: N37S #1aaq 2.5 dimer (a2) - 2 chains given [99]; N37S variant; 1 hydroxyethylene isostere and 1 HOH; pre-release file #1hhp 2.7 dimer (a2) - 1 chain given [99]; N37S variant #1hiv 2.0 dimer + peptide (a2 + s) - 3 chains given [99, 5]; N37S variant, I3V chemical modification; oxygen covalently bound to Cys 67s; 1 naphthyloxyacetyl, 1 cyclohexyl ala-psi (CHOH-CHOH)-val, 1 2- aminomethyl-pyridine, and 90 HOHs #1hos 2.3 dimer (a2) - 2 chains [99]; N37S variant; type I, BH10; 1 (1R)- di-(2-phenyl-1-carbobensyloxyvalyl-amino)ethyl-phosphinic acid and 27 HOHs #1hvp --- dimer + peptide (a2 + s) - 3 chains [99, 7]; non-experimental; N37S variant; substrate #2hvp 3.0 CA dimer (a2) - 1 chain given [99]; strain NY5 #3hvp 2.8 dimer (a2) - 1 chain given [99]; 2 Cys residues replaced by ABA; K14R, R41K, L63P, and I63V variant #4hvp 2.3 dimer + inhibitor (a2 + i) - 3 chains given [99, 6]; K14R, R41K, L63P, and I63V variant; 1 N-acetyl-thr-ile-nle-nle-gln-arg-amide; 2 Cys residues per chain replaced by ABA, 2 norleucines, 1 ter- minal amide, and 70 HOHs #5hvp 2.0 dimer + inhibitor (a2 + i) - 3 chains given [99, 6]; 1 ace-pep- statin; Ny5 strain; 2 Cl-s and 170 HOHs; #7hvp 2.4 dimer + inhibitor (a2 + i) - 3 chains given [99, 9]; K14R, R41K, L63P, and I63V variant; 4 ABAs, 1 methylene, 1 methoxy, and 95 HOHs #8hvp 2.5 dimer + inhibitor (a2 + i) - 3 chains given [99, 7]; K14R, R41K, L63P, and I64V variant; 4 ABAs, 1 leu-psi(CHOH-CH2)-val, and 80 HOHs #9hvp 2.8 dimer + inhibitor (a2 + i) - 3 chains given [99, 5]; Ny5 variant; 1 (2S,4S)-2,4-diamino-1,5-diphenyl- 3-hydroxypentane, and 1 HOH #3phv 2.7 dimer (a2) - 1 chain given [99]; isolate HXB2; N37S variant #4phv 2.10 dimer (a2) - 1 chain given [99]; Ny5 variant; 2 N,N-bis(2R- hydroxy-1(S)-indanyl)-2,6-(R,R)-diphenylmethyl-4-hydroxy-1,7- heptandiamides and 104 HOHs HIV-1 Reverse Transcriptase (HIV I) (1hrh.A: 1hrh.A) {a/b/a doubly wound anti beta ud/ud + a/b/c doubly wound para ud/cr} #1hmi 3.0 CA dimer (ab) + dsDNA - 4 chains given [556, 430, 19, 18]; C280S mutant #1hrh 2.4 monomer - 2 chains given [136]; ribonuclease H domain, represents residues 427 - 556 of full protein #1hvt 3.5 CA monomer [918]; completely unrefined; sequence UNK; many residues incomplete and/or missing HIV-2 Protease (HIV II) (2mip.A: 2mip.A [5hvp.A]) {Greek anti beta + anti beta + alpha} [virus_prot+] 3 layer 3 loop #1ivp 2.5 dimer + inhibitor (a2 + i) - 3 chains given [99, 5]; K57L mutant; 1 naphthyl-oxyacetyl-His-[cyclohexyl Ala-psi(CHOH-CHOH)-Val]-Ile- [2-amino-methyl-pyridine] and 41 HOHs #1ivq 2.6 dimer + inhibitor (a2 + i) - 3 chains given [99, 5]; K57L mutant; 1 [quinoline-2-carbonyl]-Asn-[cyclohexyl Ala-Psi(CHOH- CH2)-Val]-neopentylamine and 46 HOHs #2mip 2.2 dimer + inhibitor (2a2 + 4i) - 8 chains given [99, 6]; 4 ter- minal amides and 90 HOHs #1phv --- dimer + inhibitor (a2 + i) - 3 chains given [99, 6]; 2 statines and 1 HOH; non-experimental #2phv --- dimer + inhibitor (a2 + i) - 3 chains given [99, 8]; 1 renin inhibitor; non-experimental Human Enhancer Binding Protein MBP-1 (Homo sapiens) (1bbo: 1zaa.C [1znf] [1ard]) {domain 1: 1-27: a/b open face anti beta ud} [finger+] {domain 2: 28-57: a/b open face anti beta ud} [finger+] #1bbo NMR monomer - 60 models given [57]; C11ABU mutant; 1 ABA and 2 Zn++s Hyaluronic Acid (synthetic & Homo sapiens) #1hya 3.0 1 chain [6]; GCU NAG GCU NAG GCU NAG; NOT PROTEIN; 3 Na+s #2hya 3.0 1 chain [8]; GCU NAG GCU NAG GCU NAG GCU NAG; NOT PROTEIN; 4 Na+s #3hya 3.0 1 chain [8]; GCU NAG GCU NAG GCU NAG GCU NAG; NOT PROTEIN; 4 Na+s and 8 HOHs #4hya 3.0 1 chain [6]; NAG GCU NAG GCU NAG GCU; NOT PROTEIN; 3 Ca++s and 9 HOHs Hybrid: Chymotrypsin Inhibitor 2 and Subtilisin (Hordeum vulgare and Bacillus licheniformis) (1cis: 2ci2.I [1egl]) {a/b/c doubly wound para beta ud/ud + anti beta} #1cis NMR monomer - 15 models given [66] Hydrophobic Protein (Glycine max) (1hyp: 1hyp) {SS rich Greek anti alpha} #1hyp 1.8 monomer? [80]; 59 HOHs; 4 SSs p-Hydroxybenzoate Hydroxylase (Pseudomonas aeruginosa) {domain 1: 1-72,97-181,267-352: a/b/b doubly wound para beta ud/cr + anti alpha + anti beta} [fad_nadh] XXX check with 3grs {domain 2: 73-96,353-394: wedge alpha + anti beta + alpha} XXX {domain 3: 182-266: a/b open face anti beta cr} 1dob 2.0 monomer? [394]; 1 FAD, 1 PHB, and 159 HOHs p-Hydroxybenzoate Hydroxylase (Pseudomonas fluorescens) (1phh: 1phh) {domain 1: 1-72,97-181,267-352: a/b/b doubly wound para beta ud/cr + anti alpha + anti beta} [fad_nadh] XXX check with 3grs {domain 2: 73-96,353-394: wedge alpha + anti beta + alpha} XXX {domain 3: 182-266: a/b open face anti beta cr} #1phh 2.3 dimer (a2) - 1 chain given [394]; 1 FAD, 1 3,4-dihydroxy-ben- zoate, and 273 HOHs #2phh 2.7 dimer (a2) - 1 chain given [394]; 1 adenosine-5-diphosphoribose, 1 p-hydroxybenzoate, and 57 HOHs Ice Nucleation Protein (Pseudomonas syringae) (1ina: 1ina) {3 facing anti beta fingers} #1ina --- monomer? [535]; 3 fragments of protein - 46 residues; model of typical repeat #1inb --- monomer? [535]; 3 fragments of protein - 46 residues; model of protein-ice interface IgE Receptor, Low-Affinity FCERII/CD23 (Homo sapiens) (1hli: 1hli [2msb.A]) {a/b/a doubly wound anti beta ud/ud + open face anti beta + open face anti beta + coil} #1hli --- monomer [113]; model; 2 SSs IgE Receptor, Low-Affinity FCERII/CD23 (Mus musculus) (1hlj: 1hli [2msb.A]) {a/b/a doubly wound anti beta ud/ud + open face anti beta + open face anti beta + coil} #1hlj --- monomer [113]; model; 2 SSs Note for Immunoglobulins: XXX Domain 1 of each chain is a 4 loop; domain 2 is a standard 3 loop Greek. Immunoglobulin Carcinogenic Embryo Antigen Antibody (Mus musculus) (1aag.H:) {Greek anti beta + alpha} [igb+] (1aag.L:) {Greek anti beta} [igb+] #1aag --- dimer (ab) - 2 chains given [103, 121]; model; 2 SSs Immunoglobulin Fab Fragment BV04-01 (Mus musculus) (1nbv.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-121: Greek anti beta + alpha} [igb+] {domain 2: 122-219: Greek anti beta + alpha} [igb+] (1nbv.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-112: Greek anti beta + alpha} [igb+] {domain 2: 113-219: Greek anti beta + alpha} [igb+] #1nbv 2.0 dimer (ab) - 2 chains given [219, 219]; 5 SSs Immunoglobulin Fab Fragment of Anti-Phenylarsonate Antibody 36-71 (Mus musculus) (6fab.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-120: Greek anti beta} [igb+] {domain 2: 121-222: Greek anti beta + alpha} [igb+] (6fab.L: 6fab.L [8fab.A] [1ige.A] [8fab.B]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] #6fab 1.9 dimer (ab) - 2 chains given [214, 209]; 70 HOHs; 4 SSs Immunoglobulin Fab Fragment of Monoclonal Antibody 3D6 (Homo sapiens) Anti-HIV I-GP41 (1dfb.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-125: Greek anti beta} [igb+] {domain 2: 126-229: Greek anti beta + alpha} [igb+] (1dfb.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-105: Greek anti beta} [igb+] {domain 2: 106-212: Greek anti beta + alpha} [igb+] #1dfb 2.7 dimer (ab) - 2 chains given [212, 229]; 5 SSs Immunoglobulin Fab Fragment of 8F5 Anti-HRV2 Antibody (Mus musculus) (1bbd.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-118: Greek anti beta + alpha} [igb+] {domain 2: 119-218: Greek anti beta} [igb+] (1bbd.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-219: Greek anti beta + alphas} [igb+] #1bbd 2.8 dimer (ab) - 2 chains given [220, 218]; 1 SO4 and 5 HOHs; 4 SSs Immunoglobulin Fab/Fv Fragment of Humanized Antibody 4D5 (engineered sequence) (1fvd.B: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-120: Greek anti beta + alpha} [igb+] {domain 2: 121-214: Greek anti beta + alpha} [igb+] (1fvd.A: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-223: Greek anti beta + alpha} [igb+] #1fvc 2.2 dimer (ab) - 4 chains given [109, 113]; variant 8; Fv fragment; 126 HOHs; 4 SSs #1fvd 2.4 dimer (ab) - 4 chains given [214, 223]; variant 4; Fab fragment; 199 HOHs; 10 SSs #1fve 2.7 dimer (ab) - 4 chains given [214, 223]; variant 7; Fab fragment; 51 HOHs; 10 SSs Immunoglobulin IgG1 Fab Fragment HC19 (Mus musculus) (1gig.H: {domain 1: 1-122: Greek anti beta} [igb+] {domain 2: 123-221: Greek anti beta} [igb+] (1gig.L: {domain 1: 1-110: Greek anti beta} [igb+] {domain 2: 110-210: Greek anti beta + alphas} [igb+] #1gig 2.3 dimer (ab) - 2 chains given [210, 221]; 91 HOHs; 4 SSs Immunoglobulin Fab Fragment of Monoclonal Antibody TE33 (Mus musculus) (1tet.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-213: Greek anti beta} [igb+] (1tet.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-211: Greek anti beta + alphas} [igb+] #1tet 2.3 dimer (ab) + peptide - 3 chains given [216, 210, 15]; 1 citrate and 151 HOHs; 4 SSs Immunoglobulin Fab Fragment of Monoclonal Antibody AN02 (Mus musculus) (1baf.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-115: Greek anti beta + alpha} [igb+] {domain 2: 116-250: Greek anti beta} [igb+] (1baf.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 107-214: Greek anti beta + alpha} [igb+] #1baf 2.9 dimer (ab) - 2 chains given [214, 217]; 1 hapten, 2,2,6,6-tetra methyl-1-oxy-4-((2,4-dinitro-5-ethyldiaminyl)phenylamino)dinitro- phenyl; 5 SSs Immunoglobulin Fab Antigen-Binding Monoclonal Antibody YST9.1 (Mus Musculus) IgG2B, Kappa (1mam.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-119: Greek anti beta + alpha} [igb+] {domain 2: 120-217: Greek anti beta} [igb+] (1mam.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] #1mam 2.45 dimer (ab) - 2 chains given [214, 217]; 4 SSs Immunoglobulin Fab Fragment of Autoantibody BV04-01 (Mus musculus) (1cbv.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-121: Greek anti beta + alpha} [igb+] {domain 2: 122-219: Greek anti beta + alpha} [igb+] (1cbv.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-112: Greek anti beta} [igb+] {domain 2: 113-219: Greek anti beta + alpha} [igb+] #1cbv 2.66 dimer (ab) + ssDNA - 3 chains given [219, 219, 3]; 5 SSs Immunoglobulin Fab Fragment J539 (Mus musculus) IgA, Kappa (2fbj.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-118: Greek anti beta + alpha} [igb] {domain 2: 119-220: Greek anti beta} [igb] (2fbj.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-106: Greek anti beta} [igb] {domain 2: 107-213: Greek anti beta + alpha} [igb] #2fbj 1.95 dimer (ab) - 2 chains given [213, 220]; supersedes 1fbj; 4 NAGs, 1 FUC, 1 Zn++, and 375 HOHs; 5 SSs Immunoglobulin Fab Fragment MC/PC603 (Mus musculus) IgA, Kappa (1mcp.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-123: Greek anti beta + alpha} [igb] {domain 2: 124-222: Greek anti beta} [igb+] (1mcp.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-113: Greek anti beta} [igb] {domain 2: 114-220: Greek anti beta + alpha} [igb+] #2imm 2.00 monomer [114]; VL - variable domain of Kappa light chain; 1 ACY, 1 SO4, and 121 HOHs #2imn 1.97 monomer [113]; VL - variable domain of Kappa light chain, with complementary determining region from MOPC167; some residues deleted; 1 ACY, 1 SO4, and 120 HOHs #1mcp 2.7 dimer (ab) - 2 chains given [220, 222]; Fab fragment; 1 SO4 and 138 HOHs #2mcp 3.1 dimer (LH) - 2 chains given [220, 222]; Fab fragment; 1 phospho- choline; 5 SSs Immunoglobulin IgG1 Fab Fragmant (Mus musculus) #1gig 2.3 XXXXXXXXXXXXXXXXXXX Immunoglobulin IgG1 KOL (Homo sapiens) (2fb4.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-118: Greek anti beta + alpha} [igb] {domain 2: 119-231: Greek anti beta + alpha} [igb] XXX Thornton Greek 2 (1fc1.A: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 3: 238-337: Greek anti beta + alphas} [igb+] 3 loop {domain 4: 338-444: Greek anti beta + alphas} [igb+] 3 loop (2fb4.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-109: Greek anti beta + alpha} [igb] {domain 2: 110-214: Greek anti beta + alpha} [igb] #2fb4 1.9 dimer (ab) - 2 chains given [216, 229]; supersedes 1fb4; H chain is truncated from 2ig2; 105 HOHs; 6 SSs #1fc1 2.9 dimer (a2) - 2 chains given [224]; 2 FUCs, 2 GALs, 6 MANs, and 8 NAGs; H chain only; 6 SSs #1fc2 2.8 dimer (a2) + protein A, fragment B antigen - 2 chains given [224, 58]; half of Ig given; 1 FUC, 1 GAL, 3 MANs, 4 NAGs, and 1 sul- fate; H chain only; 2 SSs #2ig2 3.0 dimer (ab) - 2 chains given [216, 455]; supersedes 1ig2; some of sequence is taken from 1fc1; no Fc coordinates; 6 SSs Immunoglobulin IgG1 MCG (Homo sapiens) (1mco.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-118: Greek anti beta + alpha} [igb+] {domain 2: 119-218: Greek anti beta} [igb+] {domain 3: 219-322: Greek anti beta + alpha} [igb+] 3 loop {domain 4: 323-428: Greek anti beta + alpha} [igb+] 3 loop (1mco.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-216: Greek anti beta + alpha} [igb+] #1mco 3.2 dimer (ab) - 2 chains given [216, 428]; hinge deletion; 4 NAGs, 1 FUC, 3 MANs, 1 GAL, 1 sialic acid; 6 SSs Immunoglobulin Fab Fragment of Anti-Lysozyme Antibody D1.3 (Mus musculus) IgG1(Kappa) (1fdl.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-115: Greek anti beta + alpha} [igb+] {domain 2: 116-218: Greek anti beta} [igb+] (1fdl.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] #1fdl 2.5 dimer (ab) + lysozyme antigen - 3 chains given [214, 218, 129]; 9 SSs Immunoglobulin Fab Fragment Hy/Hel-10 (Mus musculus) IgG1, Kappa (3hfm.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-215: Greek anti beta} [igb+] (3hfm.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] #1hfm --- dimer (ab) - 2 chains [107, 113]; non-experimental; chain L: 2 residues differ from 2hfm and 3hfm #2hfm --- dimer + antigen (ab + g) - 3 chains [107, 113, 129]; non-ex- perimental; 4 SSs #3hfm 3.0 dimer (ab) + lysozyme antigen - 3 chains given [214, 215, 129]; 1 HOH; 9 SSs Immunoglobulin Fab' Fragment (Mus musculus) IgG1, Kappa #1fig 3.0 dimer (ab) - 2 chains given [215, 216]; 1 TSA and 1 HOH; 4 SSs Immunoglobulin Fab Fragment Hy/Hel-5 (Mus musculus) IgG1 (2hfl.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-116: Greek anti beta} [igb+] {domain 2: 117-213: Greek anti beta} [igb+] (2hfl.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-105: Greek anti beta} [igb+] {domain 2: 106-212: Greek anti beta + alpha} [igb+] #2hfl 2.54 dimer (ab) + lysozyme antigen - 3 chains given [212, 213, 129]; 8 SSs Immunoglobulin Fab Fragment (Fab 17/IA) (Mus musculus) IgG2a (1for.H: {domain 1: 1-119: Greek anti beta} [igb+] {domain 2: 120-219: Greek anti beta} [igb+] (1for.L: {domain 1: 1-106: Greek anti beta} [igb+] {domain 2: 107-210: Greek anti beta + alphas} [igb+] #1for 2.75 dimer (ab) - 2 chains given [210, 219]; 157 HOHs; 4 SSs Immunoglobulin Fab Fragment (Fab 17/9) (Mus musculus) IgG2a (1hil.B: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta + alpha} [igb+] {domain 2: 114-228: Greek anti beta} [igb+] (1hil.A: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-211: Greek anti beta + alpha} [igb+] #1hil 2.0 dimer (ab) - 4 chains given [217, 220]; 160 HOHs; 8 SSs #1him 2.9 dimer + hemagglutinin peptide (LH + a) - 6 chains given [217, 220, 8]; 2 terminal amides; 8 SSs #1hin 3.1 dimer + hemagglutinin peptide (LH + a) - 3 chains given [217, 220, 8]; 22 HOHs; 4 SSs #1ifh 2.8 dimer (ab) + peptide - 3 chains given [218, 220, 8]; peptide from influenza hemagglutinin HA1, residues 101-107; 1 HOH; 4 SSs Immunoglobulin Fab Fragment 4-4-20 (Mus musculus) IgG2a, Kappa (4fab.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-118: Greek anti beta + alpha} [igb+] {domain 2: 119-216: Greek anti beta + alpha} [igb+] (4fab.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-112: Greek anti beta} [igb+] {domain 2: 113-219: Greek anti beta + alpha} [igb+] #4fab 2.7 dimer (ab) - 2 chains [219, 216]; 1 fluorescein (antigen) and 1 2-methyl-2,4-pentanediol; 5 SSs Immunoglobulin Fab Fragment 26/9 (Mus musculus) IgG2a, Kappa (1igi.H: {domain 1: 218-337: Greek anti beta + alpha} [igb+] {domain 2: 338-437: Greek anti beta} [igb+] (1igi.L: {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-217: Greek anti beta + alphas} [igb+] #1frg 2.8 dimer + peptide (ab + p) - 2 chains given [217, 220, 10]; 1 NH2 and 1 HOH; 3 SSs Immunoglobulin Fab Fragment 26-10 (Mus musculus) IgG2a, Kappa (1igi.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 2-113: Greek anti beta + alpha} [igb+] {domain 2: 114-227: Greek anti beta} [igb+] (1igi.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-213: Greek anti beta + alpha} [igb+] #1igi 2.7 dimer (ab) - 2 chains [219, 218]; 4 SSs #1igj 2.5 dimer (ab) - 4 chains [219, 218]; 2 digoxins; 8 SSs #1maj NMR fragment - 15 models given [113]; energy minimized structures; VL fragment; 1 SS #1mak NMR fragment - 15 models given [113]; simulated annealing structures; VL fragment; 1 SS Immunoglobulin Fab' Fragment of Monoclonal Antibody DB3 (Mus musculus) IgG1 2A, Kappa 1 (1dbb.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-112: Greek anti beta} [igb+] {domain 2: 113-219: Greek anti beta} [igb+] (1dbb.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-211: Greek anti beta + alpha} [igb+] #1dba 2.8 dimer (ab) - 2 chains given [216, 219]; 2 ethanols; 4 SSs #1dbb 2.7 dimer (ab) - 2 chains given [216, 219]; 1 progesterone; 4 SSs #1dbj 2.7 dimer (ab) - 2 chains given [216, 219]; 1 aetiocholanolone and 1 HOH; 4 SSs #1dbk 3.0 dimer (ab) - 2 chains given [216, 219]; 1 5-beta-androstane- 3,17-dione and 2 HOHs; 4 SSs #2dbl 2.9 dimer (ab) - 2 chains given [216, 219]; 1 5-alpha-pregnane-3- beta-OL-hemisuccinate; 4 SSs #1dbm 2.7 dimer (ab) - 2 chains given [216, 219]; 1 progesterone-11-alpha- OL-hemisuccinate; 4 SSs Immunoglobulin NC41 Fab Complex (Mus musculus?) (1nca.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta} [igb+] {domain 2: 114-227: Greek anti beta} [igb+] (1nca.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] DUP1nca 2.5 dimer (ab) + neuraminidase avian antigen - 3 chains given [214, 221, 389]; wt; 1 Ca++, 4 NAGs, 4 MANs, and 72 HOHs; 14 SSs DUP1ncb 2.5 dimer (ab) + neuraminidase avian antigen - 3 chains given [214, 221, 389]; 1 Ca++, 5 NAGs, 4 MANs, and 72 HOHs DUP1ncc 2.5 dimer (ab) + neuraminidase avian antigen - 3 chains given [221, 214, 389]; H:E56K, K91T, and L116V mutant; 1 Ca++, 4 NAGs, and 4 MANs DUP1ncd 2.9 dimer (ab) + neuraminidase whale antigen - 3 chains given [221, 214, 389]; 1 Ca++, 5 NAGs, 4 MANs, and 69 HOHs Immunoglobulin Fab' Fragment Monoclonal Antibody B72.3 (Homo sapiens/Mus musculus Chimera) (1bbj.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-114: Greek anti beta + alpha} [igb+] {domain 2: 115-212: Greek anti beta} [igb+] (1bbj.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-211: Greek anti beta + alpha} [igb+] #1bbj 3.1 dimer (ab) - 2 chains given [211, 212]; 4 SSs Immunoglobulin Fab Fragment 50.1 (Mus musculus, strain ASW) IgG2a (1ggb.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta} [igb] {domain 2: 114-228: Greek anti beta} [igb] (1ggb.H: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb] {domain 2: 108-211: Greek anti beta + alpha} [igb] #1ggb 2.8 dimer (ab) - 2 chains given [215, 215]; diff crystal from 1ggc; 4 SSs #1ggc 2.8 dimer (ab) - 2 chains given [215, 215]; diff crystal from 1ggb; 4 SSs #1ggi 2.8 dimer + peptide (ab + a) - 6 chains given [218, 222, 16]; residues 311-328 of HIV-1 GP120 peptide, MN isolate; 8 SSs Immunoglobulin IgG1 Fab Fragment (59.1) (Mus musculus, strain BALB/C) (1acy.H: {domain 1: 1-113: Greek anti beta + alpha} [igb+] {domain 2: 114-226: Greek anti beta} [igb+] (1acy.L: {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-211: Greek anti beta + alpha} [igb+] #1acy 3.0 dimer (ab) + fragment - 3 chains given [215, 221, 24]; 5 SSs Immunoglobulin Fab Fragment of Monoclonal Anti-Arsonate Antibody, R19.9 (Mus musculus) IgG2b, Kappa (1fai.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-124: Greek anti beta + alpha} [igb] {domain 2: 125-221: Greek anti beta} [igb] (1fai.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb] {domain 2: 108-214: Greek anti beta + alpha} [igb] #2f19 2.8 dimer (ab) - 2 chains given [214, 221]; supersedes 1f19; crystal form I; 5 SSs #1fai 2.7 dimer (ab) - 2 chains given [214, 221]; crystal form II; 5 SSs Immunoglobulin Fab Fragment of Monoclonal Anti-Arsonate Antibody, R19.9 (Mus musculus) IgG2b, Kappa (1cgs.H: ) {domain 1: 1-114: Greek anti beta + alpha} [igb] {domain 2: 115-214: Greek anti beta} [igb] (1cgs.L: ) {domain 1: 1-112: Greek anti beta} [igb] {domain 2: 113-219: Greek anti beta + alphas} [igb] #1cgs 2.6 dimer (ab) - 2 chains given [219, 214]; 5 SSs Immunoglobulin Fab Fragment (Lambda, HIL) (Homo sapiens) IgG1 (8fab.B: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-119: Greek anti beta + alpha} [igb] {domain 2: 120-223: Greek anti beta + alpha} [igb] (8fab.A: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 3-106: Greek anti beta} [igb] {domain 2: 107-208: Greek anti beta + alpha} [igb] #8fab 1.8 dimer (ab) - 4 chains given [212, 224]; 668 HOHs; 8 SSs Immunoglobulin SE155-4 (Mus musculus) (1mfa. .1: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (1mfa. .2: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: L1-111: Greek anti beta + alpha} [igb+] {domain 2: H251-367: Greek anti beta + alpha} [igb+] (1mfe.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: H251-368: Greek anti beta + alpha} [igb] {domain 2: H369-468: Greek anti beta} [igb] (1mfe.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: L1-110: Greek anti beta} [igb] {domain 2: L111-211: Greek anti beta + alpha} [igb] #1mfa 1.7 monomer of joined LH chains - 1 chain given [247]; Fv fragment; 1 GAL, 1 O1-methyl-mannose, 1 abequose, and 174 HOHs; 2 SSs #1mfb 2.1 dimer (ab) - 2 chains given [215, 219]; Fab fragment; 2 GALs, 2 MANs 1 abequose, 2 rhamnoses, and 256 HOHs; 4 SSs #1mfc 2.1 dimer (ab) - 2 chains given [215, 219]; Fab fragment; 1 GAL, 1 MAN, 1 abequose, 1 rhamnoses and 195 HOHs; 4 SSs #1mfd 2.1 dimer (ab) - 2 chains given [215, 219]; Fab fragment; 1 GAL, 1 O1-methyl-mannose, 1 abequose, and 85 HOHs; 4 SSs #1mfe 2.0 dimer (ab) - 2 chains given [215, 219]; Fab fragment; 1 GAL, 1 MAN, 1 abequose, and 184 HOHs; 4 SSs Immunoglobulin IgG(Lambda) Fab' New (Homo sapiens) (7fab.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-117: Greek anti beta} [igb] {domain 2: 118-217: Greek anti beta} [igb] (7fab.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-103: Greek anti beta} [igb] {domain 2: 104-204: Greek anti beta + alpha} [igb] #7fab 2.0 dimer (ab) - 2 chains given [208, 217]; supersedes 3fab; 4 SSs Immunoglobulin IgG1 Fab' B13I2 (Mus musculus) (1igf.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-113: Greek anti beta + alpha} [igb+] {domain 2: 114-227: Greek anti beta} [igb+] (1igf.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-214: Greek anti beta + alpha} [igb+] #1igf 2.8 dimer (ab) - 4 chains given [219, 221]; 1 NAG; 8 SSs #2igf 2.8 dimer + peptide (ab + s) - 3 chains given [219, 221, 19]; 1 NAG; peptide is segment of 2mhr; 4 SSs Immunoglobulin Fab' Fragment CHA255 (Mus musculus, strain BALB/C) IgG1-Lambda (1ind.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {domain 1: 1-112: Greek anti beta + alpha} [igb+] {domain 2: 113-213: Greek anti beta} [igb+] (1ind.L: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 2-109: Greek anti beta} [igb+] {domain 2: 110-212: Greek anti beta + alpha} [igb+] #1ind 2.2 dimer (ab) - 2 chains given [215, 226]; 1 In+++, 1 4-[N'- (2-hydroxyethyl)-thioureido]-L-benzyl-EDTA, and 145 HOHs; 4 SSs #1ine 2.8 dimer (ab) - 2 chains given [215, 226]; 1 Fe+++, 1 4-[N'- (2-hydroxyethyl)-thioureido]-L-benzyl-EDTA, and 142 HOHs; 4 SSs Immunoglobulin Fab Heterologous Light Chain Dimer (Homo sapiens) (1mcw.M: see 2mcg.1) (1mcw.W: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: W1-111: Greek anti beta + alpha} [igb+] {domain 2: W112-216: Greek anti beta + alpha} [igb+] #1mcw 3.5 dimer (ab) - 2 chains given [216, 216]; hybrid of Weir; 4 SSs Immunoglobulin Fab Bence/Jones Protein (Homo sapiens) (2rhe: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {Greek anti beta} [igb] XXX Thornton Greek 2 #2rhe 1.6 dimer (a2) - 1 chain given [114]; lambda; variable domain; super- sedes 1rhe; 186 HOHs; 1 SS Immunoglobulin Lambda Light Chain Dimer (Homo sapiens) (2mcg.1: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-110: Greek anti beta + alpha} [igb+] {domain 2: 111-216: Greek anti beta + alpha} [igb+] #1mcb 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 5]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-OH; 5 SSs #1mcc 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 5]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-NH2; 5 SSs #1mcd 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 5]; peptide is N-acetyl-D-Phe-beta-Ala-L-His-D-Pro-NH2; 1 beta-alanine and 1 terminal amide; 5 SSs #1mce 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 6]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-beta-Ala-OH; 1 beta-alanine; 5 SSs #1mcf 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 7]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-beta-Ala-beta-Ala-OH; 2 beta- alanines; 5 SSs #2mcg 2.0 dimer (a2) - 2 chains given [216]; trigonal form (deionized HOH); supersedes 1mcg; 318 HOHs; 5 SSs #3mcg 2.0 dimer (a2) - 2 chains given [216]; orthorhombic form (ammonium sulfate - high salt); 5 SSs #1mch 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 7]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-beta-Ala-beta-Ala-OH; 2 beta- alanines; 5 SSs #1mci 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 4]; peptide is N-acetyl-D-Phe-L-His-D-Pro-OH; 5 SSs #1mcj 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 5]; peptide is N-acetyl-D-Phe-L-His-D-Pro-NH2; 1 terminal amide; 5 SSs #1mck 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 5]; peptide is N-acetyl-D-Glu-L-His-D-Pro-NH2; 1 terminal amide and 4 HOHs; 5 SSs #1mcl 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 3]; peptide is N-acetyl-D-His-L-Pro-OH; 5 SSs #1mcn 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 4]; peptide is N-acetyl-D-His-L-Pro-NH2; 1 terminal amide; 5 SSs #1mcq 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 4]; peptide is N-acetyl-L-His-D-Pro-NH2; 1 terminal amide; 5 SSs #1mcr 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 3]; peptide is N-acetyl-L-His-D-Pro-OH; 5 SSs #1mcs 2.7 dimer + peptide (a2 + p) - 3 chains given [216, 4]; peptide is N-acetyl-L-Gln-D-Phe-L-His-D-Pro-OH; 5 SSs Immunoglobulin Bence/Jones Protein Loc (Homo sapiens) (2bjl.1: 8fab.A [8fab.B] [1ige.A] [6fab.L]) {domain 1: 1-110: Greek anti beta + alpha} [igb+] {domain 2: 111-217: Greek anti beta + alpha} [igb+] #1bjl 3.0 dimer (a2) - 2 chains given [217]; crystalized from ammonium sulfate; light chain dimer; 5 SSs #2bjl 2.8 dimer (a2) - 2 chains given [217]; crystalized from distilled HOH; light chain dimer; 5 SSs Immunoglobulin IgG(Kappa) Fab Bence/Jones REI (Homo sapiens) (1rei.A: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {Greek anti beta} [igb] #1rei 2.0 dimer (a2) - 2 chains given [107]; variable portion of protein; 53 HOHs; 2 SSs Immunoglobulin pFc' Fragment (Cavia porcellus) IgG1 (1pfc: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {Greek anti beta + alpha} [igb] 3 loop #1pfc 3.125 dimer (a2) - 1 chain given [113]; 1 SS Immunoglobulin Fc Fragment (Homo sapiens) IgE'/CL (1ige.A: 1ige.A [8fab.B] [8fab.A] [6fab.L]) {domain 1: 1-107: Greek anti beta} [igb+] {domain 2: 108-210: Greek anti beta + alpha} [igb+] {domain 3: 211-322: Greek anti beta + alpha} [igb+] #1ige --- dimer (a2) - 2 chains [322]; non-experimental model; different SS bonds from 2ige; 2 FUCs, 2 GALs, 6 MANs, and 8 NAGs; 8 SSs #2ige --- dimer (a2) - 2 chains [322]; non-experimental model; different SS bonds from 1ige; 2 FUCs, 2 GALs, 6 MANs, and 8 NAGs; 6 SSs Immunoglobulin Fv Fragment (Homo sapiens) Ig-M (1igm.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (1igm.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: H1-129: Greek anti beta + alpha} [igb+] 4 loop {domain 2: L1-115: Greek anti beta} [igb+] 4 loop #1igm 2.3 dimer (ab) - 2 chains given [115, 129]; 147 HOHs; 2 SSs Immunoglobulin Fv Fragment Anti-Alpha1->6 Dextran 19.1.2 (Mus musculus) IgA (2fvb.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (2fvb.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: H1-119: Greek anti beta} [igb+] {domain 2: L1-106: Greek anti beta} [igb+] #1fvb --- dimer (ab) - 2 chains [106, 119]; non-experimental; 2 SSs #2fvb --- dimer (ab) - 2 chains [106, 119]; non-experimental; energy minimized model; 2 SSs Immunoglobulin Fv Fragment Anti-Alpha 1->6 Dextran W3129 (Mus musculus) IgA (2fvw.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (2fvw.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: H1-121: Greek anti beta} [igb+] {domain 2: L1-112: Greek anti beta} [igb+] #1fvw --- dimer (ab) - 2 chains [112, 121]; non-experimental; 2 SSs #2fvw --- dimer (ab) - 2 chains [112, 121]; non-experimental; energy minimized model; 2 SSs Immunoglobulin Fv Fragment of Humanized Anti-CD18 Antibody H52 (Synthetic) (1fgv.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) {Greek anti beta} [igb+] (1fgv.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {Greek anti beta} [igb+] #1fgv 1.9 dimer (ab) - 2 chains given [109, 124]; 109 HOHs; 2 SSs Immunoglobulin Fv Fragment Anti-Hen Egg Lysozyme Antibody D11.15 (Mus musculus) IgG1, Kappa (1jhl.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (1jhl.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: H1-116: Greek anti beta + alpha} [igb+] 4 loop {domain 2: L1-108: Greek anti beta} [igb+] 4 loop #1jhl 2.4 dimer (ab) + lysozyme - 3 chains given [108, 116, 129]; 6 SSs Immunoglobulin Fv Fragment of NPN43C9 (Mus musculus) (1mig.H: 8fab.B [8fab.A] [1ige.A] [6fab.L]) (1mig.L: 6fab.L [8fab.B] [8fab.A] [1ige.A]) {domain 1: H1-112: Greek anti beta} [igb+] 4 loop {domain 2: L1-107: Greek anti beta} [igb+] 4 loop #1mig --- dimer (ab) - 2 chains given [113, 117]; 1 nitrophenyl group, 1 phosphonamidate group, 1 formanilide group, and 1 butanoic acid; 2 SSs Inositol Monophosphatase (Homo sapiens) (2hhm.A: 2hhm.A) {domain 1: 5-147: a/b open face anti beta ud + alphas} {domain 2: 148-276: a/b/a doubly wound anti beta ud/ud + a/b/a doubly wound para beta ud/ud} #2hhm 2.1 dimer (a2) - 2 chains given [276]; 2 Gd+++s, 2 SO4s, and 237 HOHs Insulin (Bos taurus) Insulin is produced & stored as a hexamer of dimers, but active as a dimer. (1aph.A: 4ins.A [2gf1] [4ins.B]) (1aph.B: see 4ins.B) {SS rich a/a open face anti alpha cr + 1/2 anti beta} #1aph 2.0 dodecamer (6ab) - 2 chains given [21, 30]; 0.1M salt solution at pH 7; 1 1,2-dichloroethane and 56 HOHs; 3 SSs #1bph 2.0 dodecamer (6ab) - 2 chains given [21, 30]; 0.1M salt solution at pH 9; 1 1,2-dichloroethane and 55 HOHs; 3 SSs #1cph 1.9 dodecamer (6ab) - 2 chains given [21, 30]; 0.1M salt solution at pH 10; 1 1,2-dichloroethane and 66 HOHs; 3 SSs #1dph 1.9 dodecamer (6ab) - 2 chains given [21, 30]; cubic; 0.1M salt solu- tion at pH 11; 1 1,2-dichloroethane, 1 Na, and 60 HOHs; 3 SSs #2ins 2.5 dodecamer (6ab) - 4 chains given [21, 29]; Des-Phe B1; 2 Zn++s and 184 HOHs; 6 SSs Insulin (Homo sapiens) (1trz.A: see 4ins.A) (1trz.B: 4ins.B [4ins.A] [2gf1]) {SS rich a/a open face anti alpha cr + 1/2 anti beta} #1hiq NMR dimer? (ab) - 10 models of 2 chains given [21, 30]; B:F24S mutant; model 1 is considered a representative model; 3 SSs #1his NMR dimer? (ab) - 15 models with 2 chains each [21, 25]; DES(B26-B30) mutant; model 0 is considered a representative model; 3 SSs #1hit NMR dimer? (ab) - 9 models with 2 chains each [21, 30]; F24G mutant; model 0 is considered a representative model; 3 SSs #1hiu NMR dimer? (ab) - 11 models with 2 chains each [21, 30]; model 1 is considered a representative model; 33 SSs #1trz 1.6 dimer (ab) - 4 chains given [21, 30]; 2 Zn++s, 2 Cl-s, 1 Na+, and 123 HOHs; 6 SSs Insulin (Sus scrofa) Insulin is produced & stored as a hexamer of dimers, but active as a dimer. (4ins.A: 4ins.A [2gf1] [4ins.B]) (4ins.B: 4ins.B [4ins.A] [2gf1]) {SS rich a/a open face anti alpha cr + 1/2 anti beta} #3ins 1.5 dodecamer (6ab) - 4 chains given [21, 30]; joint x-ray & neutron scattering; 2 Zn++s and 325 deuterated HOHs; 6 SSs #4ins 1.5 dodecamer - 4 chains given [21, 30]; supersedes 1ins; 2 Zn++s and 350 HOHs; HOHs display in incorrect positions; 6 SSs #6ins 2.0 dodecamer? - 4 chains given [50]; desB30; subunits linked; 2 Zn++s and 179 HOHs; 6 SSs #7ins 2.0 dodecamer + clupeine Z peptide (6ab + p) - 7 chains given [21, 30, 31]; 1 Zn++, 3 m-cresols, and 109 HOHs; 9 SSs #9ins 1.7 dodecamer (6ab) - 2 chains given [21, 30]; cubic crystal form; 81 HOHs; 3 SSs #1iza 2.5 dodecamer (6ab) - 4 chains given [21, 30]; B:E13Q mutant; 79 HOHs; 6 SSs #1izb 2.0 dodecamer (6ab) - 4 chains given [21, 30]; B:E13Q mutant; 2 Zn++s and 125 HOHs; 6 SSs Insulin-like Growth Factor I (Somatomedin) (Homo sapiens) (2gf1: 2gf1 [4ins.A] [4ins.B]) {SS rich a/a open face anti alpha cr + coil} #1gf1 --- monomer [70]; non-experimental model; 3 SSs #2gf1 NMR monomer [70]; minimized average structure; 3 SSs #3gf1 NMR monomer - 10 models given [70]; 3 SSs Insulin-like Growth Factor II (Somatomedin) (Homo sapiens) (1gf2: 2gf1 [4ins.A] [4ins.B]) {SS rich a/a open face anti alpha cr + anti betas} #1gf2 --- monomer? - 1 chain [67]; non-experimental model; 3 SSs Integrase (Avian sarcoma virus) #1vsd 1.70 dimer (a2) - 1 chain given [152]; 1 OHE; 1 Mg++, 1 EPE, and 173 HOHs #1vse #1vsf Interferon Beta (Mus musculus) (1ifa: 1ifa) {up down anti alpha 5 helix bundle} #1ifa 2.6 CA monomer [158]; recombinant form Interferon Gamma (Bos taurus) (1rfb.A: 1rfb.A) {up down anti alpha + crossed alpha} XXX check dimer not monomer Cynthia or {dimer domain 1: A:1-84,B:85-123: 2 anti parallel anti alpha sheets} {dimer domain 2: A:85-123,B:1-84: 2 anti parallel anti alpha sheets} #1rfb 3.0 dimer (a2) - 2 chains given [119]; 43 HOHs; helices poorly formed Interferon Gamma (Homo sapiens) (1hig.A: 1rfb.A) {up down anti alpha + crossed alpha} XXX check dimer not monomer Cynthia or {dimer domain 1: A:1-84,B:85-123: 2 anti parallel anti alpha sheets} {dimer domain 2: A:85-123,B:1-84: 2 anti parallel anti alpha sheets} #1hig 3.5 CA dimer - 4 chains given [138] Interferon Gamma (Oryctolagus cuniculus) (2rig: 1rfb.A) {up down anti alpha + crossed alpha} XXX check dimer not monomer Cynthia or {dimer domain 1: A:1-84,B:85-119: 2 anti parallel anti alpha sheets} {dimer domain 2: A:85-119,B:1-84: 2 anti parallel anti alpha sheets} #2rig 2.3 CA dimer - 1 chain given [144]; supersedes 1rig Interleukin 1 Alpha (Homo sapiens) (2ila: 2ila) {up down anti beta barrel + anti beta caps} [il+] #2ila 2.3 CA monomer? [155]; D33A variant #1ita --- monomer? [151]; non-experimental model Interleukin 1 Beta (Homo sapiens) (2i1b: 2i1b) {up down anti beta barrel + anti beta caps} [il] #21bi 2.0 monomer [153]; C71A mutant #31bi 2.0 monomer [153]; C71S mutant #41bi 2.9 monomer [153]; C8A mutant #1hib 2.4 monomer [153]; T9G mutant; 113 HOHs #1i1b 2.0 monomer [153]; 83 HOHs; diff struct by diff group #2i1b 2.0 monomer [153]; 168 HOHs; diff struct by diff group #4i1b 2.0 monomer [153]; 91 HOHs; diff struct by diff group #5i1b 2.1 monomer [153]; 100 HOHs; diff struct by diff group #6i1b NMR monomer [153]; minimized average structure; 7 HOHs #7i1b NMR monomer - 32 models given [153]; 7 HOHs Interleukin 1 Beta (Mus musculus) (8i1b: 2i1b) {up down anti beta barrel + anti beta caps} [il+] [il+] #2mib 2.84 monomer [152]; 42 HOHs #8i1b 2.4 monomer [152]; 86 HOHs Interleukin 2 (Homo sapiens) (3ink.C: 3ink.C) {up down anti alpha 4 helix bundle + anti beta} XXX beta crossover #3ink 2.5 dimer? (a2) - 2 chains given [133]; C125A mutant; 2 SSs Interleukin 4 (Homo sapiens) (1rcb: 1rcb) {up down anti alpha 4 helix bundle + anti beta} #1bbn NMR monomer [133]; minimized average structure; 3 SSs #1bcn NMR monomer - 22 models given [133]; 3 SSs #1cyl NMR monomer - 20 models given [129]; 3 SSs #2int 2.4 monomer [129]; 3 SSs #1iti NMR monomer - 31 models given [133]; model 0 is restrained energy minimized average; INS(-3 to 0 EAEA), N42D, and N109D mutant #1itl NMR monomer [130]; energy minimized average; 0Met mutant; 3 SSs #1rcb 2.25 monomer [129]; 33 HOHs; 3 SSs Interleukin 8 Beta (Homo sapiens) (3il8: 3il8 [1mca.A] [1plf.A]) {SS rich ac/b open face anti beta cr} *good for pict of subst c for a #1il8 NMR dimer (a2) - 2 chains given [72]; energy minimized average; 4 SSs #2il8 NMR dimer (a2) - 30 models of 2 chains given [72]; header says there are 41 models, but only 30 are in file; 4 SSs #3il8 2.0 dimer (a2) - 1 chain given [72]; 135 HOHs Iota Carrageenan (Rhodophycae) #1car 3.0 monomer? - 2 chains given [6]; polysaccharide; NOT PROTEIN Isocitrate Dehydrogenase (Escherichia coli) (3icd: 3icd [1ipd]) {domain 1: 3-124,320-416: a/b/a doubly wound para beta ud/ud + up down mixed alpha + alpha} {domain 2: 125-319: a/b/a doubly wound para beta ud/ud + anti beta + alpha} [icd] #3icd 2.5 dimer (a2) - 1 chain given [416]; 108 HOHs #4icd 2.5 dimer (a2) - 1 chain given [416]; 1 phosphate bonded to S113 and 143 HOHs #5icd 2.5 dimer (a2) - 1 chain given [416]; 1 Mg++, 1 isocitrate, and 64 HOHs #6icd 2.8 dimer (a2) - 1 chain given [416]; S113D mutant; 1 HOH #7icd 2.4 dimer (a2) - 1 chain given [416]; S113E mutant; 66 HOHs #8icd 2.5 dimer (a2) - 1 chain given [416]; S113E mutant; 1 Mg++, 1 isocitrate, and 64 HOHs #9icd 2.5 dimer (a2) - 1 chain given [416]; 1 NAP+ and 101 HOHs 3-Isopropylmalate Dehydrogenase (Thermus thermophilus HB8) (1ipd: 1ipd [3icd]) {domain 1: 1-98,254-345: a/b/a doubly wound para beta ud/ud + up down mixed alpha + alpha} {domain 2: 99-253: a/b/a doubly wound para beta ud/ud + anti beta} [icd+] #1ipd 2.2 dimer (a2) - 1 chain given [345]; 2 SO4s and 61 HOHs Kallikrein A (Sus scrofa) (2pka.A: 1ton [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1sgt] [1hne.E]) (2pka.B: 1ton [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1sgt] [1hne.E]) {domain 1: A:16-A95B,B95Y-127,B232-246: Greek anti beta + alpha} {domain 2: B:128-231: Greek anti beta} [s_prot+] #2kai 2.5 monomer (cleaved - 2 subunit names) + inhibitor BPTI - 3 chains given [80, 152, 58]; 10 HOHs; 8 SSs #2pka 2.05 monomer (cleaved - 2 subunit names) - 4 chains given [80, 152]; 2 benzamidines and 85 HOHs; 10 SSs Kedarcidin (Actinomyces, strain L585-6) {Greek anti beta + anti betas} #1akp NMR monomer - 15 models of 1 chain given [114]; apo; 2 SSs Keratan Sulfate (Bos taurus) #1kes 3.0 polysaccharide; NOT PROTEIN; 1 chain [4] 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase (Pseudomona putida) (1kga: ???) {a/b singly wound para beta} [barrel+] #1kga 3.5 CA trimer (a3) - 1 chain given [219]; all residues UNK Kistrin (Agkistrodon rhodostoma) (1kst: 1kst [2ech]) {SS rich anti beta + coil} #1kst NMR monomer - 8 models given [68]; 6 SSs L7/L12 50S Ribosomal Protein (Escherichia coli, MRE 600) (1ctf: 1ctf) {a/b open face anti beta + crossed alpha} [ctf] XXX Thornton beta open sandwich #1ctf 1.7 fragment [74]; whole protein is a dimer, but N terminus thought to be required; C terminal domain only; 1 SO4 and 62 HOHs LAC Repressor (Escherichia coli, Strain BMH 74-12) (1lcc.A: 1lcc.A) {crossed alpha} #1lcc NMR fragment + dsDNA (a + cd) - 3 chains given [51, 11, 11]; mini- mized average structure; left half of operator; 1 Na+ and 53 HOHs #1lcd NMR fragment + dsDNA (a + cd) - 3 models of 3 chains given [51, 11, 11]; left half of operator; 1 Na+ and 53 HOHs Alpha Lactalbumin (Papio cynocephalus) (1alc: 1alc [1hel]) {domain 1: 1-36,101-122: crossed alpha} encircled axial alpha {domain 2: 37-100: c/b open face anti beta ud + alpha} [lzm] #1alc 1.7 monomer [123]; sequence deduced from x-ray; 1 Ca++ and 150 HOHs; 4 SSs Beta Lactamase (Bacillus lichenformis 749/C) (4blm.A: 4blm.A [3blm]) {domain 1: 31-70,215-291: a/b/c doubly wound anti beta cr/cr} {domain 2: 71-214: encirclied axial alpha ud+cr + anti beta coil} [blm+] #2blm 2.0 CA monomer - 2 chains given [265] #4blm 2.0 monomer - 2 chains given [265]; missing FORMUL records #1mbl 2.0 monomer - 2 chains given [256]; E166A mutant; 2 SO4s and 579 HOHs Beta Lactamase (Staphylococcus aureus PC1) (3blm: 3blm [4blm.A]) {domain 1: 31-70,216-290: a/b/c doubly wound anti beta cr/cr} {domain 2: 71-215: encirclied axial alpha ud+cr + anti beta coil} [blm] #1blc 2.2 monomer [257]; 1 N-(1-carboxy-2-oxy-3-hydroxybutyl)-N-(3-oxy-cis- propenyl)amine, 1 N-(2-oxy-3-hydroxybutyl)-N-(3-oxy-transpro- penyl)amine, and 324 HOHs #1blh 2.3 monomer [257]; 1 FOS and 195 HOHs #1blp 2.3 monomer [257]; D179N mutant; 126 HOHs #3blm 2.0 monomer [257]; supersedes 1blm; 207 HOHs L-Lactate Dehydrogenase (Bacillus stearothermophilus) (1ldb: 1ldn.A [1lld.A] [6ldh] [2cmd] [4mdh.A]) {domain 1: 15-161,246-264: a/b/a doubly wound para beta ud/ud} {domain 2: 162-245,265-331: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd] #1ldb 2.8 tetramer (a4) - 1 chain given [317]; apo; 2 SO4s and 1 HOH #2ldb 3.0 tetramer (a4) - 1 chain given [317]; 1 NAD, 1 FBP, 2 SO4s, and 50 HOHs #1ldn 2.5 tetramer (a4) - 8 chains given [316]; 8 oxamates, 8 NADHs, 4 FBPs, and 572 HOHs L-Lactate Dehydrogenase (Bifidobacterium longum, AM101-2) (1lld.A: 1lld.A [1ldn.A] [6ldh] [2cmd] [4mdh.A]) {domain 1: 7-148,234-255: a/b/a doubly wound para beta ud/ud} {domain 2: 149-233,256-319: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd+] #1lld 2.0 tetramer (a4) - 2 chains given [319]; C199S mutant; T-state; 2 NADs and 222 HOHs L-Lactate Dehydrogenase (Lactobacillus casei) (1llc: 1ldn.A [1lld.A] [6ldh] [2cmd] [4mdh.A]) {domain 1: 13-163,246-263: a/b/a doubly wound para beta ud/ud} {domain 2: 164-245,264-334: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd] #1llc 3.0 tetramer (a4) - 1 chain given [325]; complex with CO2; 1 FBP and 1 SO4 Lactate Dehydrogenase (Mus musculus) (2ldx: 6ldh [1ldn.A] [1lld.A] [2cmd] [4mdh.A]) {domain 1: 1-161,247-266: a/b/a doubly wound para beta ud/ud} {domain 2: 162-246,267-331: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd] #2ldx 2.96 tetramer (a4) - 1 chain given [331]; isoenzyme C4; apo; super- sedes 1ldx; 31 HOHs Lactate Dehydrogenase (Squalus acanthias) (6ldh: 6ldh [1ldn.A] [1lld.A] [2cmd] [4mdh.A]) {domain 1: 0-161,245-264: a/b/ac doubly wound para beta ud/ud} {domain 2: 162-244,265-329: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd] #3ldh 3.0 tetramer (a4) - 1 chain given [330]; M4; 1 NAD and 1 pyruvate; sequence is substantially different from all others in this entry and should be used with caution #6ldh 2.0 tetramer (a4) - 1 chain given [330]; M4; apo; supersedes 4ldh; 2 SO4s and 286 HOHs #8ldh 2.8 tetramer (a4) - 1 chain given [330]; M4; apo; 2 citrates and 281 HOHs #1ldm 2.1 tetramer (a4) - 1 chain given [329]; M4; no ACE at N terminus; 1 NAD, 2 oxamates, and 245 HOHs Heart Lactate Dehydrogenase (Sus scrofa) (5ldh: 6ldh [1ldn.A] [1lld.A] [2cmd] [4mdh.A]) {domain 1: 0-165,240-263: a/b/ac doubly wound para beta ud/ud} {domain 2: 166-239,264-331: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd] #5ldh 2.7 tetramer (a4) - 1 chain given [334]; H4 - heart; 1 S-Lac-NAD+ cofactor and 1 citrate Muscle Lactate Dehydrogenase (Sus scrofa) (9ldt.A: 6ldh [1ldn.A] [1lld.A] [2cmd] [4mdh.A]) {domain 1: 0-165,246-265: a/b/ac doubly wound para beta ud/ud} {domain 2: 166-245,266-331: a/b/ac doubly wound anti beta ud/ud+cr + open face anti beta} [nbd+] #9ldb 2.2 tetramer (a4) - 2 chains given [332]; muscle; 2 NADs, 1 oxamate, 3 SO4s, and 152 HOHs #9ldt 2.0 tetramer (a4) - 2 chains given [332]; muscle; 2 NADs, 2 oxamates, 2 SO4s, and 154 HOHs Lactoferrin (Homo sapiens) (1lfg: 1lfg [1ovb]) {domain 1: 1-90,247-344: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/ud + wedge alpha} {domain 2: 91-246: a/b/ac doubly wound mixed beta} {domain 3: 345-432,595-691: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/ud + wedge alpha} {domain 4: 433-594: a/b/ac doubly wound mixed beta} #1lct 2.0 fragment [333]; N-terminal half of protein; deglycosylated prior to crystallization; 1 Fe+++, 1 carbonate, and 186 HOHs; 6 SSs #1lfg 2.2 monomer? [691]; 2 Fe+++s, 2 carbonates, 3 NAGS, 2 FUCs, and 493 HOHs; 16 SSs #1lfh 2.8 monomer? [691]; apo; 1 Cl- and 373 HOHs; 16 SSs #1lfi 2.1 monomer? [691]; 2 Cu++s, 2 carbonates, 3 NAGs, 2 FUCs, and 301 HOHs; 16 SSs Lactose Repressor Protein (Escherichia coli) (1ltp.L: 1ltp.L) {domain 1: 62-160,307-323: a/b/a doubly wound para beta ud/ud} {domain 2: 161-306: a/b/a doubly wound para beta ud/ud} #1ltp --- fragment [262]; model of core domain Lambda Repressor (Phage lambda) (1lmb.3: 1lmb.3) {a/a/a doubly wound para alpha cr/cr} [repressor] XXX Cynthia check #1lrp 3.2 CA dimer (a2) - 1 chain given [92]; N-terminal domain #1lmb 1.8 dimer + operator dsDNA (a2 + d2) - 4 chains given [92, 20]; supersedes 1lrd; 140 HOHs S-Lectin (Bos taurus) (1slt.A: 1slt.A) {Greek anti beta} XXX ududcc + ccudu [[lectin]] minimal #1slt 1.9 dimer (a2) - 2 chains given [134]; 6 oxygens bound to Cys's, 2 NAGs, 2 GALs, 1 Cl-, and 154 HOHs Lectin (Erythrina corallodendron) (1lte: 1lte [2ctv.A] [1lec] [2ltn.A] [2ltn.B]) {Greek anti beta} XXX extra strand plus curls, then ududcc + ccudu [[lectin]] #1lte 2.0 dimer (a2) - 1 chain given [239]; 2 NAGs, 1 FUC, 3 MANs, 1 XYL, 1 Mn++, 1 Ca++, 1 GLC, 1 GAL, and 100 HOHs Lectin IV (Griffonia simplicifolia) (1lec: 1lec [2ctv.A] [1lte] [2ltn.A] [2ltn.B]) {Greek anti beta} XXX extra strand plus curls, then ududcc + ccudu [[lectin]] #1lec 2.0 monomer? [243]; 1 Mn++, 1 Ca++, 2 NAGs, 1 FUC, 1 SO4, and 143 HOHs #1led 2.0 monomer? [243]; with Lewis B human blood group determinant; 1 Mn++, 1 Ca++, 3 NAGs, 3 FUCs, 1 GAL, 1 SO4, and 144 HOHs Lectin (Lens culinaris) (1len.A: 2ltn.A [2ctv.A] [1lec] [1lte] [2ltn.B]) {Greek anti beta} XXX extra strand plus curls, then ududcc + ccudu [[lectin]] #2lal 1.8 tetramer (2ab) - 4 chains given [181, 52]; 2 Ca++s, 2 Mn++s, 2 phosphates, and 215 HOHs #1lem 3.0 tetramer (2ab) - 2 chains given [181, 52]; hexagonal crystal form; 1 GLC, 1 Ca++, 1 Mn++, and 43 HOHs #1len 1.8 tetramer (2ab) - 4 chains given [181, 52]; monoclinic crystal form; 2 phosphates, 2 Ca++s, 2 Mn++s, and 231 HOHs Lectin (Pisum sativum) (2ltn.A: 2ltn.A [2ctv.A] [1lec] [1lte] [2ltn.B]) (2ltn.B: 2ltn.B [2ctv.A] [1lec] [1lte] [2ltn.A]) {Greek anti beta} XXX extra strand plus curls, then ududcc + ccudu [ltn] #2ltn 1.7 tetramer (a2b2) - 4 chains given [181, 52]; 2 Ca++s, 2 Mn++s, and 294 HOHs #1rin 2.6 tetramer (a2b2) - 4 chains given [180, 49]; 2 Ca++s, 2 Mn++s, 2 MANs, and 87 HOHs Leghemoglobin (Lupinus luteus l) (1lh1: 1lh1) {Greek anti alpha} [globin] XXX two layer anti alpha crossed to anti alpha For these entries, the 1s & 2s of a pair were refined in diff. manners. #1lh1 2.0 monomer [153]; supersedes 1hbl; 1 HEM with Fe+++ and 1 acetate- and 69 HOHs #2lh1 2.0 monomer [153]; 1 HEM with Fe+++ and 1 acetate- and 69 HOHs #1lh2 2.0 monomer [153]; 1 HEM with Fe+++ and HOH and 67 HOHs #2lh2 2.0 monomer [153]; 1 HEM with Fe+++ and HOH and 67 HOHs #1lh3 2.0 monomer [153]; 1 HEM with Fe+++ and CN and 66 HOHs #2lh3 2.0 monomer [153]; 1 HEM with Fe+++ and CN and 66 HOHs #1lh4 2.0 monomer [153]; deoxy; 1 HEM with Fe++ and HOH and 67 HOHs #2lh4 2.0 monomer [153]; deoxy; 1 HEM with Fe++ and HOH and 67 HOHs #1lh5 2.0 monomer [153]; 1 HEM with Fe+++ and F and 67 HOHs #2lh5 2.0 monomer [153]; 1 HEM with Fe+++ and F and 67 HOHs #1lh6 2.0 monomer [153]; 1 HEM with Fe+++ and nicotinate- and 65 HOHs #2lh6 2.0 monomer [153]; 1 HEM with Fe+++ and nicotinate- and 65 HOHs #1lh7 2.0 monomer [153]; 1 HEM with Fe++ and nitrosobenzene and 64 HOHs #2lh7 2.0 monomer [153]; 1 HEM with Fe++ and nitrosobenzene and 64 HOHs Leucine Aminopeptidase (Bos taurus) (1lap: 1lap) {domain 1: 1-173: a/b/a doubly wound beta ud/ud} {domain 2: 174-484: a/b/a doubly wound mixed beta ud/ud + anti beta + crossed alpha} #1bll 2.4 hexamer? (a6) + inhibitor - 2 chains given [479, 5]; inhibitor is (2S,3R)3-amino-2-hydroxyl-5-methyl-hexanoyl-L-Val-L-Val-L-Asp; 2 Zn++s and 132 HOHs #1bpm 2.9 hexamer? (a6) - 1 chain given [488]; 1 Zn++ and 1 Mg++ #1bpn 2.9 hexamer? (a6) - 1 chain given [488]; 2 Zn++s #1lap 2.7 hexamer (a6) - 1 chain given [488]; 2 Zns Leucine Binding Protein (Escherichia coli, strain K12) (2lbp: 2liv) {domain 1: 1-120,251-328: a/b/a doubly wound para beta + anti beta + wedge alphas} {domain 2: 121-250,329-346: a/b/a doubly wound para beta + anti beta} [binding] #2lbp 2.4 monomer [346]; 91 HOHs; 1 SS Leucine/Isoleucine/Valine Binding Protein (Escherichia coli) (2liv: 2liv) {domain 1: 1-120,251-326: a/b/a doubly wound para beta + anti beta + wedge alphas} {domain 2: 121-250,327-344: a/b/a doubly wound para beta + anti beta} [binding] XXX Thornton dw3 #2liv 2.4 monomer [344]; 121 HOHs; 1 SS Leucocyte Elastase Inhibitor (Equus caballus) (1hle.A: 1hle.A [1ova.A] [2ach.A] [7api.A] [1pai.A] [1hle.B]) (1hle.B: 1hle.B [1ova.A] [2ach.A] [7api.A] [1pai.A] [1hle.A]) {domain 1: 22-53,200-290,361-391: ac/b/a doubly wound anti beta ud/ud} {domain 2: 54-199,291-358: a/b/b doubly wound anti beta ud+cr/cr} XXX Cynthia check #1hle 1.95 monomer (cleaved) - 2 chains given [346, 31]; 1 Ca++ and 212 HOHs Lipase (Candida rugosa) (1crl: 1thg [1ace]) {domain 1: 1-59,94-247,312-339,416-515: a/b doubly wound para beta + anti betas} XXX {domain 2: 60-93: wedge alpha + coil} {domain 3: 248-311: wedge alpha + alpha + coil} {domain 4: 340-415,516-534: crossed alpha} #1crl 2.06 monomer? [534]; 3 NAGs and 310 HOHs; 2 SSs #1trh 2.1 monomer? [534]; 2 NAGs and 301 HOHs; 2 SSs Lipase (Geotrichum candidum, strain ATCC 34514) (1thg: 1thg [1ace]) {domain 1: a/b/a doubly wound para beta} XXX #1thg 1.8 monomer [544]; 4 NAGs and 343 HOHs; 2 SSs Lignin Peroxidase (Phanerochaete chrysosporium) (1lga.A: 1lga.A [1arp]) {domain 1: 9-152: Greek anti alpha} XXX {domain 2: 153-344: crossed alpha + wedge alpha + coil} XXX #1lga 2.03 monomer - 2 chains given [343]; 2 HEMs with Fe+++, 2 NAGs, 4 Ca++s, and 474 HOHs; 8 SSs Lipoamide Dehydrogenase (Pseudomonas fluorescens) (1lpf.A: 3lad.A [3grs] [2tpr.A] [1lvl] [1npx]) {domain 1: 1-151,282-348: a/b/bc doubly wound para beta ud/cr + crossed alpha} {domain 2: 152-281: a/b/b doubly wound para beta ud/cr} {domain 3: 349-480: a/b open face anti beta ud + alpha} [fad_nadh+] #1lpf 2.8 dimer (a2) - 2 chains given [472]; 2 FADs; 2 SSs Luciferase (Vibrio harveyi) {barrel} #1brl 2.4 dimer (ab) - 2 chains given [355, 324]; 1 PO4 and 73 HOHs Lysin (Haliotis rufescens) (1lis: 1lis) {schief alpha + alpha crossover} XXX nomenclature #1lis 1.9 monomer? [136]; 84 HOHs Lysozyme (Bacteriophage T4) (3lzm: 3lzm) {domain 1: 1-11,62-164: encircled axial alpha ud+cr} {domain 2: 12-60: a/b open face anti beta ud} or XXX Cynthia look {domain 1: a/a/a doubly wound anti alpha ud/cr} or {domain 1: up down anti alpha 5 helix bundle + crossed alpha + schief alpha} [lzm-] grouping seems questionable #1dya 1.90 monomer [164]; V131D mutant; 2 SEOs, 2 Cl-s, and 139 HOHs #1dyb 1.75 monomer [164]; V131G mutant; 2 SEOs, 2 Cl-s, and 139 HOHs #1dyc 2.1 monomer [164]; V131I mutant; 1 SEO, 2 Cl-s, and 132 HOHs #1dyd 2.1 monomer [164]; V131L mutant; 2 SEOs, 2 Cl-s, and 145 HOHs #1dye 1.8 monomer [164]; V131S mutant; 1 SEO, 2 Cl-s, and 143 HOHs #1dyf 1.9 monomer [164]; V131M mutant; 2 SEOs, 2 Cl-s, and 131 HOHs #1dyg 2.1 monomer [164]; V131E mutant; 2 SEOs, 2 Cl-s, and 131 HOHs #1lyd 2.0 monomer [164]; synthetic coding; 82 HOHs #1lye 1.8 monomer [162]; C54T, T59V, C97A mutant; 2 SEOs, 2 Cl-s, and 144 HOHs #1lyf 1.8 monomer [162]; C54T, T59S, C97A mutant; 2 SEOs, 2 Cl-s, and 144 HOHs #1lyg 1.8 monomer [162]; C54T, T59N, C97A mutant; 2 SEOs, 2 Cl-s, and 132 HOHs #1lyh 1.7 monomer [162]; C54T, T59G, C97A mutant; 2 SEOs, 2 Cl-s, and 142 HOHs #1lyi 2.0 monomer [162]; C54T, T59D, C97A mutant; 2 SEOs, 2 Cl-s, and 135 HOHs #1lyj 1.8 monomer [162]; C54T, T59A, C97A mutant; 2 SEOs, 2 Cl-s, and 143 HOHs #2lzm 1.7 monomer [164]; supersedes 1lzm; 118 HOHs #3lzm 1.7 monomer [164]; same as 2lzm, but better refinement; use as basis for comparison of 1lxx mutants; 152 HOHs #4lzm 1.7 monomer [164]; high salt; 1 SEO, 2 Cl-s, and 139 HOHs #5lzm 1.8 monomer [164]; medium salt; 3 SEOs, 2 Cl-s, and 119 HOHs #6lzm 1.8 monomer [164]; low salt; 3 SEOs, 2 Cl-s, and 94 HOHs #7lzm 1.8 monomer [164]; dithiothreitol; 2 Cl-s and 137 HOHs #201l 2.0 monomer - 2 chains given [164]; Ins(K48-HP), C54T, C97A mutant; 2 SEOs and 120 HOHs #102l ---> mutants and variants of T4 lysozyme #102l 1.74 INS(N40-A), C54T, C97A; 2 SEOs, 2 Cl-s, and 132 HOHs #103l 1.9 INS(N40-SLD), C54T, C97A; 1 SEO, 2 Cl-s, and 128 HOHs #104l 2.8 INS(N40-AA), C54T, and C97A; 32 HOHs #205l 2.1 INS(S44-AAA), C54T, C97A; 2 SEOs, 2 Cl-s, and 114 HOHs #107l 1.80 S44G, C54T, C97A; 2 SEOs, 2 Cl-s, and 151 HOHs #108l 1.80 S44I, C54T, C97A; 2 SEOs, 2 Cl-s, and 170 HOHs #109l 1.85 S44K, C54T, C97A; 2 SEOs, 2 Cl-s, and 152 HOHs #110l 1.70 S44L, C54T, C97A; 2 SEOs, 2 Cl-s, and 137 HOHs #111l 1.80 S44N, C54T, C97A; 2 Cl-s and 161 HOHs #112l 1.80 S44P, C54T, C97A; 2 SEOs, 2 Cl-s, and 148 HOHs #113l 1.80 S44R, C54T, C97A; 2 SEOs, 2 Cl-s, and 149 HOHs #114l 1.80 S44T, C54T, C97A; 2 SEOs, 2 Cl-s, and 148 HOHs #115l 1.80 S44V, C54T, C97A; 2 SEOs, 2 Cl-s, and 144 HOHs #216l 2.10 2 chains given [164]; S44W, C54T, C97A; 22 HOHs; supersedes 116l #217l 1.70 S44E, C54T, C97A; 3 SEOs, 1 Cl-, and 177 HOHs #118l 1.80 C54T, C97A, A130S; 2 SEOs, 2 Cl-s, and 168 HOHs #119l 1.65 C54T, C97A, A134S; 2 SEOs, 2 Cl-s, and 161 HOHs #120l 1.80 A41S, C54T, C97A; 2 SEOs, 2 Cl-s, and 177 HOHs #221l 1.70 A49S, C54T, C97A; 1 SEO, 2 Cl-s, and 135 HOHs #122l 1.80 C54T, A73S, C97A; 2 SEOs, 2 Cl-s, and 161 HOHs #123l 1.80 C54T, A82S, C97A; 2 SEOs, 2 Cl-s, and 158 HOHs #224l 1.85 C54T, A93S, C97A; 1 SEO, 2 Cl-s, and 138 HOHs #125l 1.85 C54T, C97A, A98S; 2 SEOs, 2 Cl-s, and 160 HOHs #126l 1.80 C54T, C97A, V149T; 2 SEOs, 2 Cl-s, and 160 HOHs #127l 1.85 C54T, V75T, C97A; 2 SEOs, 3 Cl-s, and 166 HOHs #128l 1.70 C54T, V87T, C97A; 2 SEOs, 1 Cl-, and 162 HOHs #129l 1.7 C54T, A93T, C97A; 2 SEOs, 2 Cl-s, and 159 HOHs #130l 1.7 C54T, C97A, T151S; 2 SEOs, 2 Cl-s, and 161 HOHs #131l 1.7 T26S, C54T, C97A; 2 SEOs, 2 Cl-s, and 172 HOHs #138l 1.7 C54T, A93C, C97A; 1 SEO, 2 Cl-s, and 121 HOHs #139l 1.7 C54T, N68C, A93C, C97A; 2 SEOs, 2 Cl-s, and 146 HOHs #140l 2.10 C54T, C97A, L121A, A129M, F153L; 2 SEOs, 2 Cl-s, and 101 HOHs #141l 2.00 C54T, C97A, L121A, A129M, V149I; 2 SEOs, 2 Cl-s, and 109 HOHs #142l 2.00 C54T, C97A, L121A, A129V, L133A, F153L; 2 SEOs, 2 Cl-s, and 105 HOHs #143l 2.00 C54T, C97A, L121A, A129V, L133M, F153L; 2 SEOs, 2 Cl-s, and 106 HOHs #144l 2.10 C54T, C97A, L121I, A129L, L133M, F153W; 2 SEOs, 2 Cl-s, and 103 HOHs #145l 2.00 C54T, C97A, L121I, A129W, L133M, F153W; 2 SEOs and 76 HOHs #146l 1.85 C54T, C97A, L121M, A129L, L133M, V149I, F153W; 2 SEOs, 2 Cl-s, and 99 HOHs #147l 2.00 C54T, C97A, L121M, L133V, F153L; 2 SEOs, 1 Cl-, and 99 HOHs #1l00 1.9 Q105A; 1 SEO and 144 HOHs #1l01 1.7 T155A, T157I; 118 HOHs #1l02 1.7 T157A; 119 HOHs #1l03 1.7 T157C; 1 SEO and 152 HOHs #1l04 1.7 T157D; 118 HOHs #1l05 1.7 T157D; 118 HOHs #1l06 1.7 T157E; 118 HOHs #1l07 1.7 T157F; 119 HOHs #1l08 1.7 T157G; 119 HOHs #1l09 1.7 T157H; 118 HOHs #1l10 1.7 T157I; 119 HOHs #1l11 1.7 T157L; 1 SEO and 118 HOHs #1l12 1.7 T157N; 119 HOHs #1l13 1.7 T157R; 118 HOHs #1l14 1.7 T157S; 118 HOHs #1l15 1.7 T157V; 119 HOHs #1l16 1.7 G156D; 122 HOHs #1l17 1.7 I3V; 152 HOHs #1l18 1.7 I3Y; 153 HOHs #1l19 1.7 S38D; 151 HOHs #1l20 1.85 N144D; 152 HOHs #1l21 1.85 N55G; 154 HOHs #1l22 1.7 K124G; 153 HOHs #1l23 1.7 G77A; 152 HOHs #1l24 1.7 A82P; 151 HOHs #1l25 1.8 P86A; 152 HOHs #1l26 1.7 P86C; 1 SEO and 122 HOHs #1l27 1.8 P86D; 152 HOHs #1l28 1.9 P86G; 153 HOHs #1l29 1.7 P86H; 119 HOHs #1l30 1.7 P86L; 158 HOHs #1l31 1.8 P86R; 118 HOHs #1l32 1.7 P86S; 154 HOHs #1l33 1.7 V131A; 152 HOHs #1l34 1.9 R96H; 153 HOHs #1l35 1.8 I9C, C54T, C97A, L164C; 151 HOHs; 1 SS #1l36 1.7 E128A, V131A, N132A; 2 SEOs, 3 Cl-s and 140 HOHs #1l37 1.85 T115E; 151 HOHs #1l38 1.80 Q123E; 152 HOHs #1l39 1.85 C54T, C97A, N144E; 152 HOHs #1l40 1.85 C54T, C97A, N144E; 152 HOHs #1l41 1.75 C54T, K83H, C97A, A112D; 152 HOHs #1l42 1.80 K16E; 152 HOHs #1l43 1.80 K16E; 152 HOHs #1l44 1.70 R119E; 152 HOHs #1l45 1.70 K135E; 150 HOHs #1l46 1.70 K147E; 152 HOHs #1l47 1.70 R154E; 151 HOHs #1l48 1.7 A98V; 1 SEO and 148 HOHs #1l49 1.8 A98V, T152S; 151 HOHs #1l50 1.85 A98V, V149C, T152S; 152 HOHs #1l51 1.9 A98V, V149I, T152S; 152 HOHs #1l52 1.7 T152S; 152 HOHs #1l53 1.85 V149C; 1 SEO and 148 HOHs #1l54 1.9 C54T, C97A, M102K; 152 HOHs #1l55 1.9 C54T, D92N, C97A; 2 SEOs, 2 Cl-s, and 142 HOHs #1l56 1.8 K60P; 2 SEOs and 153 HOHs #1l57 1.9 N116D; 2 SEOs, 2 Cl-s, and 138 HOHs #1l58 1.65 P143A; 1 SEO and 151 HOHs #1l59 1.75 C54T, C97A, T109N; 1 SEO, 2 Cl-s, and 150 HOHs #1l60 1.7 G113A; 152 HOHs #1l61 1.8 S38N, C54T, C97A; 1 SEO, 2 Cl-s, and 148 HOHs #1l62 1.7 C54T, C97A, T109D; 1 SEO, 2 cl-s, and 141 HOHs #1l63 1.75 C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l64 1.9 N40A, K43A, S44A, E45A, L46A, D47A, K48A, C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l65 1.7 D47A, C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l66 1.7 K43A, C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l67 1.9 L46A, C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l68 1.7 S44A, C54T, C97A; 2 SEOs, 2 Cl-s, and 140 HOHs #1l69 1.9 L133A; 1 SEO, 2 Cl-s, and 141 HOHs #1l70 1.9 V131A, N132A; 2 SEOs, 3 Cl-s, and 138 HOHs #1l71 1.85 E128A, V131A; 1 SEO, 2 Cl-s, and 138 HOHs #1l72 1.85 D127A, E128A; 2 SEOs, 2 Cl-s, and 137 HOHs #1l73 1.85 D127A, E128A, V131A, N132A; 3 SEOs, 3 Cl-s, and 127 HOHs #1l74 1.7 E128A, V131A, N132A, L133A; 2 SEOs, 3 Cl-s, and 139 HOHs #1l75 1.9 D127A, E128A, V131A, N132A, L133A; 2 SEOs, 3 Cl-s, and 139 HOHs #1l76 1.9 C54T, D72P, C97A; 2 SEOs, 2 Cl-s, and 141 HOHs #1l77 2.05 C54T, C97A, M102L; 2 SEOs, 2 Cl-s, and 99 HOHs #2l78 2.0 C54T, C97A, V111I; 2 SEOs, 2 Cl-s, and 140 HOHs #1l79 1.9 C54T, C97A, L99F, V111I; 2 SEOs, 2 Cl-s, and 132 HOHs #1l80 1.8 C54T, C97A, L99F, M102L, V111I; 2 SEOs, 2 Cl-s, and 140 HOHs #1l81 2.0 C54T, C97A, L99F, M102L, F153L; 2 SEOs, 2 Cl-s, and 139 HOHs #1l82 2.1 C54T, C97A, L99F, M102L, V111I, F153L; 2 SEOs, 2 Cl-s, and 125 HOHs #1l83 1.70 C54T, C97A, L99A; 2 SEOs, 1 benzene, 2 Cl-s, and 142 HOHs #1l84 1.90 C54T, C97A, L99A, F153A; 2 SEOs, 1 benzene, 2 Cl-s, and 125 HOHs #1l85 2.00 C54T, C97A, F153A; 2 SEOs, 2 Cl-s, and 128 HOHs #1l86 1.80 C54T, C97A, F153I; 2 SEOs, 2 Cl-s, and 129 HOHs #1l87 1.80 C54T, C97A, F153L; 2 SEOs, 2 Cl-s, and 135 HOHs #1l88 1.85 C54T, C97A, F153M; 2 SEOs, 2 Cl-s, and 135 HOHs #1l89 1.90 C54T, C97A, L99A, F153A; 2 SEOs, 2 Cl-s, and 126 HOHs #1l90 1.75 C54T, C97A, L99A; 2 SEOs, 2 Cl-s, and 146 HOHs #1l91 1.80 C54T, C97A, L99F; 2 SEOs, 2 Cl-s, and 138 HOHs #1l92 1.70 C54T, C97A, L99I; 2 SEOs, 2 Cl-s, and 141 HOHs #1l93 1.80 C54T, C97A, L99M; 2 SEOs, 2 Cl-s, and 141 HOHs #1l94 1.80 C54T, C97A, L99V; 2 SEOs, 2 Cl-s, and 140 HOHs #1l95 2.00 C54T, C97A, F153V; 2 SEOs, 2 Cl-s, and 130 HOHs #1l96 2.0 I3P; 1 SEO, 2 Cl-s, and 139 HOHs #1l97 2.0 I3P; 201 HOHs #1l98 1.8 Q105E; 1 SEO and 165 HOHs #1l99 1.95 Q105G; 1 SEO and 134 HOHs #1tla 2.0 C54T, C97A, S117F; 1 phosphate, 2 Cl-s, and 138 HOHs Lysozyme (Coturnix coturnix japonica) (2ihl: 1hel [1alc]) {domain 1: 1-40,86-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-85: c/b open face anti beta ud} [lzm+] #2ihl 1.4 monomer? [129]; 1 Na+ and 151 HOHs; 4 SSs; 6 res diff from 1hel Lysozyme (Gallus Gallus) (1hel: 1hel [1alc]) {domain 1: 1-40,86-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-85: c/b open face anti beta ud} [lzm] #132l 1.8 monomer [129]; 6 lysines have been dimethylated; 78 HOHs; 4 SSs DUP1fdl 2.5 monomer + antibody dimer (LH) - 3 chains given [129, 214, 218]; 9 SSs #1hel 1.7 monomer [129]; recombinant form; 185 HOHs; 4 SSs #1hem 1.8 monomer [129]; recombinant form; S91T mutant; 185 HOHs; 4 SSs #1hen 1.8 monomer [129]; recombinant form; I55V and S91T mutant; 185 HOHs; 4 SSs #1heo 1.8 monomer [129]; recombinant form; I55V mutant; 185 HOHs; 4 SSs #1hep 1.8 monomer [129]; recombinant form; T40S, I55V, S91T mutant; 185 HOHs; 4 SSs #1heq 1.8 monomer [129]; recombinant form; T40S, S91T mutant; 185 HOHs; 4 SSs #1her 1.8 monomer [129]; recombinant form; T40S mutant; 185 HOHs; 4 SSs #1hew 1.75 monomer [129]; 3 NAGs and 103 HOHs; 4 SSs DUP2hfl 2.54 monomer + antibody dimer (LH) - 3 chains given [129, 212, 213]; N101D mutant; 8 SSs DUP2hfm --- monomer + antibody dimer (LH) - 3 chains [129, 107, 113]; non-ex- perimental; 4 SSs DUP3hfm 3.0 monomer + antibody dimer (LH) - 3 chains given [129, 214, 215]; 1 HOH; 9 SSs #1hwa NMR monomer [129]; minimized average structure; 4 SSs #1lma 1.75 monomer [129]; low solvent content crystal; 2 nitrates and 148 HOHs; 4 SSs #1lym 2.5 monomer - 2 chains given [129]; 8 SSs #2lym 2.0 monomer [129]; 1 atm; 1.4 M NaCl; 151 HOHs; 4 SSs #3lym 2.0 monomer [129]; 1000 atm; 1.4 M NaCl; 163 HOHs; 4 SSs #4lym 2.1 monomer [129]; "low humidity" form?; 157 HOHs; 4 SSs #3lyt 1.9 monomer - 2 chains given [129]; 100K; 406 HOHs; 8 SSs #4lyt 1.9 monomer - 2 chains given [129]; 298K; 191 HOHs; 8 SSs #5lyt 1.9 monomer [129]; 100K; 237 HOHs; 4 SSs #6lyt 1.9 monomer [129]; 298K; 100 HOHs; 4 SSs #1lyz 2.0 monomer [129]; unrefined coordinates; 97 HOHs; 4 SSs #2lyz 2.0 monomer [129]; after refinement 1; 97 HOHs; 4 SSs #3lyz 2.0 monomer [129]; different refinement; 97 HOHs; 4 SSs #4lyz 2.0 monomer [129]; different refinement; 97 HOHs; 4 SSs #5lyz 2.0 monomer [129]; different refinement; 97 HOHs; 4 SSs #6lyz 2.0 monomer [129]; different refinement; 97 HOHs; 4 SSs #7lyz 2.5 monomer [129]; triclinic crystal form; 4 SSs #8lyz 2.5 monomer [129]; iodine inactivated; 4 SSs #9lyz 2.5 substrate only [NAM-NAG-NAM] #1lzh 6.0 CA monomer - 2 chains given [129]; monoclinic #2lzh 6.0 CA monomer [129]; orthorhombic #1lzt 1.97 monomer [129]; diff refinement from 2lzt; 220 HOHs; 4 SSs #2lzt 1.97 monomer [129]; diff refinement from 1lzt; 5 nitrates and 249 HOHs; 4 SSs #1rcm 1.9 monomer - 2 chains given [129]; partially reduced; 2 carboxy- methyl groups on B:C127 and 133 HOHs; 6 SSs Lysozyme (Homo sapiens) (1lz1: 1hel [1alc]) {domain 1: 1-40,87-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-86: c/b open face anti beta ud} [lzm+] #133l 1.77 monomer [130]; R115H mutant; 72 HOHs; 4 SSs #134l 1.77 monomer [130]; R115E mutant; 71 HOHs; 4 SSs #1laa 1.77 monomer [130]; D53E mutant; 112 HOHs; 4 SSs #1lhh 1.8 monomer [130]; V110P mutant; 101 HOHs; 4 SSs #1lhi 1.8 monomer [130]; P71G mutant; 123 HOHs; 4 SSs #1lhj 1.8 monomer [130]; P103G mutant; 128 HOHs; 4 SSs #1lhk 1.8 monomer [130]; D91P mutant; 115 HOHs; 4 SSs #1lhl 1.8 monomer [130]; A47P mutant; 115 HOHs; 4 SSs #1lhm 1.8 monomer? [130]; C77A and C95A mutant; 101 HOHs; 3 SSs #2lhm 1.8 monomer? [130]; Q86D and A92D mutant; apo; experimentally intro- duced Ca binding site; 142 HOHs; 4 SSs #3lhm 1.8 monomer? [130]; Q86D and A92D mutant; holo; experimentally introduced Ca binding site; 1 Ca and 109 HOHs; 4 SSs #1lz1 1.5 monomer [130]; 4 SSs #1lz4 1.8 monomer [130]; C77A mutant; 57 HOHs; 3 SSs #1lz5 1.8 monomer [134]; 74(RGDS)75 insertion mutant; 2 Cl-s and 82 HOHs; 4 SSs #1lz6 1.8 monomer [138]; 74(TGRGDSPA)75 insertion mutant; 2 Cl-s and 160 HOHs; 4 SSs #1tay 1.70 monomer [130]; Y63A mutant; 74 HOHs; 4 SSs #1tby 1.77 monomer [130]; Y63L mutant; 77 HOHs; 4 SSs #1tcy 1.70 monomer [130]; Y63F mutant; 75 HOHs; 4 SSs #1tdy 1.70 monomer [130]; Y63W mutant; 74 HOHs; 4 SSs Lysozyme (Meleagris gallopavo) (135l: 1hel [1alc]) {domain 1: 1-40,86-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-85: c/b open face anti beta} [lzm+] #135l 1.30 monomer [129]; 114 HOHs; 4 SSs; 7 res diff from 1hel #1lz2 2.8 CA monomer [129]; 5 residues differ from 2lz2 #2lz2 2.2 monomer [129]; 111 HOHs; 4 SSs #3lz2 2.5 monomer [129]; 4 SSs #1lz3 1.5 monomer [129]; N39D, N103D variant from 135l; 75 HOHs; 4 SSs Lysozyme (Numida meleagris) (1hhl: 1hel [1alc]) {domain 1: 1-40,86-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-85: c/b open face anti beta} [lzm+] #1hhl 1.9 monomer [129]; 87 HOHs; 4 SSs Lysozyme (Phasianus colchicus) (1ghl.A: 1hel [1alc]) {domain 1: 0-40,86-129: a/a/c doubly wound crossed alpha cr/cr} XXX Cynthia look {domain 2: 41-85: c/b open face anti beta} [lzm+] #1ghl 2.1 monomer - 2 chains given [130]; 140 HOHs; 8 SSs DUP1jhl 2.4 monomer + antibody dimer - 3 chains given [108, 116, 129]; 6 SSs Macromomycin (Streptomyces macromomyceticus) (2mcm: 2mcm [1acx] [1noa]) {Greek anti beta + anti beta} [acx+] #2mcm 1.5 monomer? [112]; 3 2-methyl-2,4-pentanediol, 1 Ca++, and 120 HOHs; 2 SSs Major Urinary Protein (Mus musculus) (1mup: 1mup) {up down anti beta + coil caps + ud alpha} see 1rbp XXX Thornton orthogonal barrel+ #1mup 2.4 monomer? [166]; 2-(sec-butyl) thiazoline, 4 Cds, and 77 HOHs; 1 SS Malate Dehydrogenase (Escherichia coli) (2cmd: 2cmd [1ldn.A] [1lld.A] [6ldh] [4mdh.A]) {domain 1: 0-147,223-243: a/b/a doubly wound para beta ud/ud} {domain 2: 148-222,244-312: a/b/a doubly wound anti beta ud/ud + open face anti beta + alpha} #1cme --- monomer [312]; MODEL - based on 4mdh and crystal structure of E. coli MDH; 1 malate, 1 NAD, and 88 HOHs #2cmd 1.87 monomer [312]; 1 citrate and 94 HOHs #1emd 1.9 monomer [312]; 1 citrate, 1NAD, and 86 HOHs Cytoplasmic Malate Dehydrogenase (Sus scrofa) (4mdh.A: 4mdh.A [1ldn.A] [1lld.A] [6ldh] [2cmd]) {domain 1: 0-155,241-259: a/b/a doubly wound para beta ud/ud} {domain 2: 156-240,260-333: a/b/ac doubly wound anti beta ud/ud + open face anti beta + alpha} [nbd] #4mdh 2.5 dimer (a2) - 2 chains given [334]; supersedes 2mdh; 2 NADs, 2 SO4s, and 471 HOHs Malate Dehydrogenase (Thermus flavis, strain AT-62) {domain 1: 0-153: a/b/a doubly wound para beta ud/ud} {domain 2: 154-332: a/b/ac doubly wound anti beta ud/ud + encircled axial alpha} #1bmd 1.9 dimer (a2) - 2 chains given [327]; 2 NADs and 288 HOHs D-Maltodextrin Binding Protein (Escherichia coli) (1omp: 1omp) {domain 1: 1-113,254-332: a/b/a doubly wound mixed beta ud/ud+cr + wedge alpha} {domain 2: 150-206,333-370: anti alpha + crossed alpha} {domain 3: 114-149,207-253: a/b/ac doubly wound mixed beta ud/ud} #1dmb 1.80 monomer [370]; 1 beta-cyclodextrin and 135 HOHs #2mbp 1.7 CA monomer [370]; supersedes 1mbp; 1 D-maltose #1omp 1.8 monomer [370]; 73 HOHs Mandelate Racemase (Pseudomonas putida) (2mnr: 2mnr [1chr.A] [1mle]) {domain 1: 3-122,342-359: a/b/c doubly wound anti beta ud/ud + schief alpha + anti beta} {domain 2: 123-359: a/b singly wound para beta + coil} [barrel+] #2mnr 1.9 octamer (a8) - 1 chain given [357]; 1 Mg++, 1 SO4, and 211 HOHs #1mns 2.0 octamer (a8) - 1 chain given [357]; 1 Mg++, 1 alpha-phenyl- glycidate, and 209 HOHs Mannose Binding Protein A (Rattus rattus) (2msb.A: 2msb.A [1hli]) {a/b/a doubly wound anti beta ud/cr + c/b open face anti beta cr} #1msb 2.3 dimer (a2) - 2 chains given [115]; lectin domain; represents residues 107 - 221 of full protein; 4 Holmium ions and 57 HOHs #2msb 1.7 dimer (a2) - 2 chains given [115]; lectin domain; represents residues 107 - 221 of full protein; 6 Ca++s, 1 NAG, 6 MANs, and 211 HOHs; 4 SSs Melittin (Apis mellifera) (2mlt.A: 2mlt.A) {tetramer: up down anti alpha 4 helix bundle} [mlt] #2mlt 2.0 tetramer (a4) - 2 chains given [27]; supersedes 1mlt; 2 terminal amides, 2 SO4s, and 23 HOHs Mengo Encephalomyocarditis Virus Coat Protein (Mengo virus) (2mev.1: 2mev.1 [1tme.1]) {double stranded anti beta cylinder} [virus] XXX Thornton Jelly Roll (2mev.2: 1tme.2 [1r1a.2] [2plv.2]) {double stranded anti beta cylinder} [virus] XXX Thornton Jelly Roll (2mev.3: 1tme.3 [1bbt.3] [4rhv.3] [2plv.3]) {double stranded anti beta cylinder} [virus] XXX Thornton Jelly Roll (2mev.4: 1bbt.4) {coil + alpha} #1mec 3.2 240mer (60abcd) - 4 chains given [274, 256, 231, 70]; pH 4.6; 1:A45R and 3:V58M mutant wrt 2mev; 2 phosphates and 233 HOHs; 1 SS #2mev 3.0 240mer (60abcd) - 4 chains given [277, 256, 231, 70]; super- sedes 1mev; 1 phosphate and 233 HOHs; 1 SS Mesentericopeptidase (Bacillus mesentericus) (1mee.A: 1cse.E [1thm] [2pkc]) {a/b/a doubly wound para beta ud/ud + anti beta + crossed alpha + para alpha + coil} [sbt+] #1mee 2.0 monomer + Eglin-C inhibitor - 2 chains given [275, 64]; 2 Cas and 312 HOHs Met Repressor (Escherichia coli) (1cmb.A: 1cmb.A) {dimer: crossed alpha + anti beta + wedge alpha + coil} #1cma 2.8 dimer + dsDNA (a2 + d2) - 4 chains given [104, 10, 9]; 2 S-ade- nosylmethionines and 36 HOHs #1cmb 1.8 dimer (a2) - 2 chains given [104]; apo; 1 phosphate and 88 HOHs #1cmc 1.8 dimer (a2) - 2 chains given [104]; holo; 2 S-adenosylmethionines, 2 Mg++s, and 206 HOHs Metalloproteinase-2 (Homo sapiens) {4 X 4 anti beta wheel} #1rtg 2.6 fragment [210]; 2 Ca++, 1 Cl-, and 76 HOHs Metallothionein-2 (Homo sapiens) (1mhu: 4mt2 [1pi2]) (2mhu: 4mt2 [1pi2]) {domain 1: 1-31: metal binding coil cylinder} {domain 2: 32-61: metal binding coil cylinder} #1mhu NMR alpha domain [31]; 4 Cds #2mhu NMR beta domain [30]; 3 Cds Metallothionein-2A (Oryctolagus cuniculus) (1mrb: 4mt2 [1pi2]) (2mrb: 4mt2 [1pi2]) {domain 1: 1-31: metal binding coil cylinder} {domain 2: 32-61: metal binding coil cylinder} #1mrb NMR alpha domain [31]; 4 Cds #2mrb NMR beta domain [31]; 3 Cds Metallothionein Isoform II (Rattus rattus) (4mt2: 4mt2 [1pi2]) {domain 1: 1-31: metal binding coil cylinder} {domain 2: 32-61: metal binding coil cylinder} #1mrt NMR alpha domain [31]; 4 Cds #2mrt NMR beta domain [30]; 3 Cds #4mt2 2.0 monomer [61]; 5 Cd++s, 2 Zn++s, 1 Na+, and 69 HOHs Methionine Aminopeptidase (Escherichia coli) (1mat: 1mat) {domain 1: 2-119: a/b open face anti beta ud + anti beta} {domain 2: 120-264: a/b open face anti beta ud + anti beta} #1mat 2.4 monomer? [264]; 2 Co++s and 15 HOHs Methionyl-tRNA Synthetase (Escherichia coli) (1mea: 1mea) {metal binding crossed turns + coil} XXX #1mea NMR monomer [28]; minimized average structure; zinc binding domain; 1 Zn++ #1med NMR monomer - 11 models given [28]; zinc binding domain; 1 Zn++ Methylamine Dehydrogenase (Paracoccus denitrificans) Although name and source for 2bbk are the same as 1mda, the sequences are very different and are listed separately. (2bbk.H: 2bbk.H) {7 X 4 anti beta wheel} *good for structure picture (2bbk.L: 2bbk.L) {c/b open face anti beta cr + anti betas + coil} #2bbk 2.2 tetramer (a2b2) - 4 chains given [355, 125]; 2 oxygens bound to L:W57 and M:W57 and 556 HOHs; 14 SSs #2mta 2.4 tetramer + amicyanin + cyt C551 (a2b2 + 2c + 2d) - 4 chains given [373, 125, 105, 147]; cytochrome is not fit to electron density -- simulated from another cytochrome C551; 2 Os bound to indole ring of L:W57, 1 Cu++, 1 HEM with Fe++, 1 phosphate, and 127 HOHs; 7 SSs Methylamine Dehydrogenase (Paracoccus denitrificans) Although name and source for 1mda are the same as 2bbk, the sequences are very different and are listed separately. (1mda.H: 1mda.H [2bbk.H] [2mad.H]) {7 X 4 anti beta wheel} (1mda.L: 2bbk.L) {c/b open face anti beta cr + anti betas + coil} #1mda 2.5 tetramer + electron-transfer partner protein (a2b2 + c2) - 6 chains given [268, 121, 103]; sequences determined from electron density; 2 O2s and 2 Cu++s; 12 SSs Methylamine Dehydrogenase (Thiobacillus versutus) (2mad.H: 2bbk.H) {7 X 4 anti beta wheel + alpha} (2mad.L: 2bbk.L) {c/b open face anti beta cr + anti betas + coil} #2mad 2.25CA tetramer (a2b2) - 2 chains given [124, 373]; supersedes 1mad; full coordinates for the L chain - CA only for the H chain; 2 Os from quinone and 86 HOHs; 7 SSs #1mae 2.8 CA tetramer (a2b2) - 2 chains given [124, 373]; full coordinates for the L chain - CA only for the H chain; 1 O of quinone, 1 N of methylhydrazine, and 85 HOHs; 7 SSs #1maf 2.6 CA tetramer (a2b2) - 2 chains given [124, 373]; full coordinates for the L chain - CA only for the H chain; 1 O of quinone, 1 N of (2,2,2)-trifluoroethylhydrazine and 85 HOHs; 7 SSs Beta-2-Microglobulin (?) (1hsa.B: 1hsa.B) {Greek anti beta} [igb] XXX Thornton Greek 2 DUP1hhg 2.6 monomer + HLA + HIV-1 peptide - 6 chains given [100, 275, 9]; residues 195-207 of HIV-1 GP120; heavy chain of HLA DUP1hhh 3.0 monomer + HLA + hepatitis B nucleocapsid peptide - 3 chains given [100, 275, 10] DUP1hhi 2.5 monomer + HLA + influenza A protein frament - 6 chains given [100, 275, 9]; heavy chain of HLA; residues 58-66 of influenza A matrix protein M1 DUP1hhj 2.5 monomer + HLA + HIV-1 reverse transcriptase peptide - 6 chains given [100, 275, 9]; heavy chain of HLA; residues 309-317 of HIV-1 reverse transcriptase DUP1hhk 2.5 monomer + HLA + HTLV-1 tax protein peptide - 6 chains given [100, 275, 9]; heavy chain of HLA; residues 11-19 of HTLV-1 tax protein DUP1hla 3.5 CA monomer + antigen A2 (a + b) - 2 chains given [97, 270]; 3 SSs DUP2hla 2.6 monomer + antigen AW 68.1 (b + a) - 2 chains given [99, 270]; 10 HOHs; 3 SSs DUP3hla 2.6 monomer + antigen A2.1 (a + b) - 2 chains given [99, 270]; 46 HOHs; A2.1; 2 additional residues at C terminus of B chain; 3 SSs DUP1hsa 2.1 monomer + antigen B*2705 + peptide (a + b + c) - 6 chains given [99, 276, 9]; 440 HOHs; 6 SSs DUP1hsb 1.9 beta-2-microglobulin + antigen AW 68.1 (b + a + 2 peptides) - 4 chains given [99, 270, 3, 2]; 270 HOHs; 3 SSs DUP1vaa 2.3 microglobulin + MHC + VSV peptide - 3 chains given [99, 274, 8]; 114 HOHs; 3 SSs DUP1vab 2.5 microglobulin + MHC + Sendai virus peptide - 3 chains given [99, 274, 9]; 91 HOHs; 3 SSs Alpha-Momorcharin (Momordica charantia) {domain 1: 1-25,37-180: a/b/a doubly wound anti beta ud/cr} {domain 2: 26-36,181-246: a/b open face anti beta ud + anti beta + alpha} #1aha 2.2 monomer? [246]; 1 adenine and 81 HOHs #1ahb 2.2 monomer? [246]; 1 formycin monophosphate and 80 HOHs #1ahc 2.0 monomer? [246]; 163 HOHs Momordin (Momordica charantia) {domain 1: 1-180: a/b/a doubly wound mixed beta ud/cr + alpha} {domain 2: 181-246: a/b open face anti beta ud + crossed alpha} #1mom 2.16 monomer? [246]; 2 NAGs and 197 HOHs Monellin (Dioscoreophyllum cumminsii Diels) (3mon.A: 3mon.A) (3mon.B: 3mon.B) {a/b open face anti beta cr} #3mon 2.8 dimer (ab) - 8 chains given [44, 50]; supersedes 1mon Monocyte Chemoattractant and Activating Protein (Homo sapiens) (1mca.A: 1mca.A [3il8] [1plf.A]) {a/b open face anti beta cr} [hla_a2+] #1mca --- dimer? (a2) - 2 chains given [73]; non-experimental; modeled after interleukin-8 MS2 Virus Coat Protein (Bacteriophage MS2) (1ms2.A: 1ms2.A) {ab/b open face anti beta cr} #1ms2 3.3 180mer (a180) - 3 chains given [129] Muconolactone Isomerase (Pseudomonas putida) (1mli: 1mli) {a/b open face anti beta ud} #1mli 3.3 CA decamer (a10) - 1 chain given [96] Cis, Cis Muconate Cycloisomerase (Pseudomonas putida) (1mle: 1mle [1chr.A] [2mnr]) {domain 1: a/b doubly wound anti beta ud/cr + anti alpha} {domain 2: a/b singly wound para beta} [barrel+] #1mle 2.5 CA decamer - 1 chain given [374]; 1 Mn Murein Lipoprotein (Escherichia coli) (1mlp.A: 1mlp.A) {para alpha} #1mlp --- dimer? (a2) - 2 chains [58]; non-experimental C-Myb Proto-Oncogene (Gallus domesticus) (1pom: 1pom) {a/a open face anti alpha} #1pom --- monomer? [51]; DNA binding domain, repeat 3; non-experimental Myeloblastosis Associated Viral Protease (Myeloblastosis Associated Virus) (1mvp.A: 2rsp.A) {Greek anti beta + alpha cap + anti beta} [virus_prot+] #1mvp 2.2 dimer (a2) - 2 chains [124]; 133 HOHs; res 82 V vs. L in 2rsp, otherwise identical #2mvp --- dimer (a2) + substrate - 3 chains [124, 10]; non-experimental model based on 1mvp and 4hvp Myeloperoxidase (Canis familiaris) (1myp.A: 1myp.A) {domain 1: up down anti alpha + crossed alpha} XXX Cynthia look {domain 2: crossed alpha + anti beta} #1myp 3.0 tetramer (2ab, cleaved) - 4 chains given [108, 466]; 1 HEM with Fe++, 12 NAGs, and 1 Ca++; 13 SSs Myoglobin (Aplysia limacina) (1mba: 1mba [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1myt] [2lhb]) {heme binding Greek anti alpha} [globin] #2fal 1.8 monomer [147]; 1 cyanide, 1 HEM with Fe+++, and 88 HOHs #2fam 1.8 monomer [147]; 1 thiocyanate, 1 HEM with Fe+++, and 93 HOHs #1mba 1.6 monomer [147]; met; pH 7.0; 1 HEM with Fe+++ and 108 HOHs #3mba 2.0 monomer [147]; pH 7.0; 1 fluoride, 1 HEM with Fe+++, and 201 HOHs #4mba 2.0 monomer [147]; pH 7.0; 1 HEM with Fe+++ and imidazole and 107 HOHs #5mba 1.9 monomer [147]; met; 1 HEM with Fe+++ and azide and 126 HOHs; supersedes 2mba Myoglobin (Equus caballus) (1ymb: 1mbd [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #1yma 2.0 monomer [153]; H64Y mutant; 1 HEM with Fe++, 1 SO4, and 129 HOHs #1ymb 1.9 monomer [153]; met; 1 HEM with Fe++, 1 SO4, and 154 HOHs #1ymc 2.0 monomer [153]; cyanomet-sulf; 1 HEM with S, 1 SO4, 1 cyanide, and 173 HOHs Myoglobin (Homo sapiens) (2mm1: 1mbd [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #2mm1 2.8 monomer [153]; K45R and C110A mutant; 1 HEM with Fe and 1 HOH and 7 HOHs Myoglobin (Phoca vitulina) (1mbs: 1mbd [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] #1mbs 2.5 monomer [153]; unusual space group A 2; 1 HEM with Fe+++ Myoglobin (Physeter catodon) (1mbd: 1mbd [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] *good for structure picture #2cmm 1.8 monomer [153]; 1 porphyrin with Fe+++; 1 cyanide and 59 HOHs #1fcs 1.6 monomer [153]; H64V and T67R mutant; 1 HEM with Fe+++, 2 sul- fates, and 120 HOHs #2mb5 1.8 monomer [153]; carbonmonoxy; neutron study; supersedes 1mb5; 1 HEM with Fe++ and CO, 5 ammoniums, 1 SO4, and 267 deuterated HOHs #1mbc 1.5 monomer [153]; FeII; carbonmonoxy; 260K; 1 HEM with Fe++ and CO, 1 SO4, and 137 HOHs #1mbd 1.4 monomer [153]; deoxy; pH 8.4; 1 HEM with Fe++, 1 SO4, and 388 HOHs #1mbi 2.0 monomer [153]; 1 HEM with Fe+++; complex with 1 IMD, 1 SO4, and 119 HOHs #1mbn 2.0 monomer [153]; ferric; met #4mbn 2.0 monomer [153]; met; supersedes 2mbn; 1 HEM with Fe+++ and HOH, 2 SO4s, and 120 HOHs #5mbn 2.0 monomer [153]; deoxy; supersedes 3mbn; 1 HEM with Fe++, 1 sul- fate, and 120 HOHs #1mbo 1.6 monomer [153]; oxy; pH 8.4; 1 HEM with Fe++ and O2, 1 SO4, and 334 HOHs #1mbw 1.9 monomer [154]; met; X0M and D122N mutant; 1 HEM with Fe+++ and H2O, 1 SO4, and 117 HOHs #2mga 2.2 monomer [154]; carbonmonoxy; -0M, H64G, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 CO, and 224 HOHs #2mgb 2.0 monomer [154]; met; -0M, H64G, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 bound HOH, and 180 HOHs #2mgc 1.9 monomer [154]; carbonmonoxy; -0M, H64L, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 CO, and 165 HOHs #2mgd 1.8 monomer [154]; deoxy; -0M, H64L, D122N mutant; 1 HEM with Fe++, 1 SO4, and 144 HOHs #2mge 1.7 monomer [154]; met; -0M, H64L, D122N mutant; 1 HEM with Fe++, 1 SO4, and 139 HOHs #2mgf 1.8 monomer [154]; carbonmonoxy; -0M, H64Q, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 CO, and 158 HOHs #2mgg 1.8 monomer [154]; deoxy; -0M, H64Q, D122N mutant; 1 HEM with Fe++, 1 SO4, and 156 HOHs #2mgh 2.0 monomer [154]; met; -0M, H64Q, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 bound HOH, and 170 HOHs #2mgi 2.0 monomer [154]; met; -0M, H64T, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 bound HOH, and 136 HOHs #2mgj 2.0 monomer [154]; met; -0M, H64V, D122N mutant; 1 HEM with Fe++, 1 SO4, and 122 HOHs #2mgk 2.0 monomer [154]; carbonmonoxy; -0M, D122N mutant; 1 HEM with Fe++, 1 SO4, 1 CO, and 149 HOHs #2mgl 2.0 monomer [154]; deoxy; -0M, D122N mutant; 1 HEM with Fe++, 1 SO4, and 168 HOHs #2mgm 1.9 monomer [154]; oxy; -0M, D122N mutant; 1 HEM with Fe++, 1 O2, 1 SO4, and 138 HOHs #1mgn 1.9 monomer [154]; -0M, D122N, H64Y mutant; 1 HEM with Fe++, 1 SO4, and 152 HOHs #2mya 2.0 monomer [153]; pH 7.0; 1 HEM with Fe++, 1 ethyl isocyanide, 1 SO4, and 162 HOHs #2myb 1.9 monomer [153]; pH 7.0; 1 HEM with Fe++, 1 methyl isocyanide, 1 SO4, and 190 HOHs #2myc 1.8 monomer [153]; pH 7.0; 1 HEM with Fe++, 1 N-butyl isocyanide, 1 SO4, and 173 HOHs #2myd 1.8 monomer [153]; pH 7.0; 1 HEM with Fe++, 1 N-propyl isocyanide, 1 SO4, and 164 HOHs #2mye 1.68 monomer [153]; pH << 7.0; 1 HEM with Fe++, 1 ethyl isocyanide, 1 SO4, and 185 HOHs #1mym 1.7 monomer [154]; carbonmonoxy; Ins(M-V1), D122N, and F46V mutant; 1 HEM with Fe++, 1 CO, 1 SO4, and 147 HOHs #1swm 1.8 monomer [153]; 1 HEM with Fe++, 1 azide, 1 SO4, and 123 HOHs #2spl 1.7 monomer [154]; carbonmonoxy; -0M, L29F, D122N mutant; 1 HEM with Fe++, 1 CO, 1 SO4, and 159 HOHs #2spm 1.7 monomer [154]; met; -0M, L29F, D122N mutant; 1 HEM with Fe++, 1 bound HOH, 1 SO4, and 112 HOHs #2spn 1.7 monomer [154]; oxy; -0M, L29F, D122N mutant; 1 HEM with Fe++, 1 O2, 1 SO4, and 124 HOHs #2spo 1.7 monomer [154]; met; -0M, L29V, D122N mutant; 1 HEM with Fe++, 1 bound HOH, 1 SO4, and 139 HOHs Myoglobin (Sus scrofa) (1pmb.A: 1mbd [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1myt] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin] #1pmb 2.5 monomer - 2 chains given [153]; aquo met; pH 7.1; 2 HEMs with Fe+++ and 57 HOHs #1myg 1.75 monomer - 2 chains given [153]; aquo met; pH 7.1; recombinant form; 2 HEMs with Fe++, 2 SO4s, and 234 HOHs #1myh 1.9 monomer - 2 chains given [153]; aquo met; pH 7.1; recombinant form; K45R mutant; 2 HEMs with Fe++, 2 SO4s, and 96 HOHs #1myi 2.0 monomer - 2 chains given [153]; aquo met; pH 7.1; recombinant form; K45S mutant; 2 HEMs with Fe++ and 122 HOHs #1myj 1.9 monomer - 2 chains given [153]; aquo met; pH 7.1; recombinant form; V68T mutant; 2 HEMs with Fe++, 2 SO4s, and 107 HOHs #1yca 2.2 monomer - 2 chains given [153]; V68T mutant; carbonmonoxy, pH 7.1; 2 HEMs with Fe++ and 107 HOHs #1ycb 2.1 monomer - 2 chains given [153]; V68T mutant; deoxy, pH 7.1; 2 HEMs with Fe++ and 109 HOHs Myoglobin (Thunnus albacares) (1myt: 1myt [2hhb.A] [2hhb.B] [2hbg] [1pbx.B] [3sdh.A] [1mbd] [1mba] [2lhb]) {heme binding Greek anti alpha} [globin+] #1myt 1.74 monomer [146]; 1 HEM with Fe++ and 81 HOHs Myohemerythrin (Themiste zostericola) (2mhr: 2mhr [2hmq.A]) {up down anti alpha 4 helix bundle} [hmr] DUP2igf 2.8 fragment + IgG dimer (s + LH) - 3 chains given [19, 219, 221, 19]; 1 NAG; 4 SSs #2mhr 1.7/1.3 monomer [118]; 1 Fe+++O--, 1 azide, and 3 SO4s Myosin Light Chain Kinase (Oryctolagus cunniculus) (2bbm.B: 2bbm.B) {alpha} DUP2bbm NMR fragment + calmodulin - 22 models of 2 chains given [26, 148]; model 1 is minimized average; 4 Ca++s DUP2bbn NMR fragment + calmodulin - 21 models of 2 chains given [26, 148]; 4 Ca++s Myosin Light Chain Kinase (Gallus gallus) DUP1cdl 2.2 fragment + calmodulin - 8 chains given [20, 147]; 16 Ca++s and 270 HOHs Myotoxin II (Phospholipase A2) (Bothrops asper) {a/a/b doubly wound para alpha ud/ud + coil} #1clp 2.8 monomer? - 2 chains given [121]; 27 HOHs; 14 SSs NADH Peroxidase (Streptococcus faecalis) (1npx: 1npx [2tpr.A] [3grs] [3lad.A] [1lvl]) {domain 1: 1-114,244-319: a/b/b doubly wound para beta ud/cr + anti betas + anti alpha} {domain 2: 115-243: a/b/b doubly wound para beta ud/ud} {domain 3: 320-447: a/b/a doubly wound anti beta ud/ud} [fad_nadh+] #1npx 2.16 tetramer (a4) - 1 chain given [447]; 3 Os bound to Cys 42, 1 FAD, and 369 HOHs #2npx 2.4 tetramer (a4) - 1 chain given [447]; 3 Os bound to Cys 42, 1 FAD, 1 NAD, and 337 HOHs Narbonin (Vicia narbonensis l.) (1nar: 1nar) {a/b singly wound para beta + anti beta} [barrel+] #1nar 1.8 monomer? [290]; 513 HOHs Neocarzinostatin (Streptomyces carzinostaticus) (1noa: 1noa [2mcm] [1acx]) {Greek anti beta + anti beta} [acx+] #1nco 1.8 monomer - 2 chains given [113]; chain A is apo, chain B is holo; 1 NCS chromophore, 1 2-methyl-2,4-pentanediol, and 161 HOHs; 4 SSs #1noa 1.5 monomer [113]; from S. c., var. F41; apo; 99 HOHs; 2 SSs Beta-Nerve Growth Factor (Mus musculus) {open face anti beta + crossed anti beta + anti beta + coil} #1bet 2.3 monomer? [107]; 32 HOHs; 3 SSs Neuraminidase (Influenza virus - subtype N2 A/Tokyo/3/67) Hydrophobic N-terminal membrane anchor removed. (2bat: 2bat [1nsc.A] [2nn9]) {6 X 4 anti beta wheel + coil cap} #2bat 2.0 tetramer (a4) - 1 chain given [388]; 1 sialic acid, 1 Ca++, 7 NAGs, 6 MANs, 1 4-SO4-N-acetylgalactosamine, 1 FUC, and 116 HOHs; 2 res differ from 1nn2; 9 SSs #1nn2 2.2 tetramer - 1 chain given [388]; 1 Ca, 9 NAGs, 6 MANs, 1 4-sul- fate-N,acetylgalactosamine, 1 FUC, and 86 HOHs; 9 SSs Neuraminidase N9-NC41 (Avian influenza virus - A/Tern/Australia/G70C/75) (2nn9: 2nn9 [1nsc.A] [2bat]) {6 X 4 anti beta wheel + coil cap} #1nca 2.5 monomer? + Fab dimer - 3 chains given [389, 214, 221]; wt; 1 Ca++, 4 NAGs, 4 MANs, and 72 HOHs; 14 SSs #1ncb 2.5 monomer? + Fab dimer - 3 chains given [389, 214, 221]; N:N329D mutant; 1 Ca++, 5 NAGs, 4 MANs, and 72 HOHs; 14 SSs #1ncc 2.5 monomer? + Fab dimer - 3 chains given [389, 214, 221]; N:I368R mutant; 1 Ca++, 4 NAGs, and 4 MANs; 14 SSs #2nn9 2.2 monomer? [388]; S370L mutant; reference structure for other mutants; 1 Ca, 4 NAGs, 5 MANs, and 93 HOHs; 9 SSs #3nn9 2.3 monomer? [388]; N329D mutant; 1 Ca, 4 NAGs, 5 MANs, and 93 HOHs; 9 SSs #4nn9 2.3 monomer? [388]; I368R mutant; 1 Ca, 4 NAGs, 5 MANs, and 89 HOHs; 9 SSs #5nn9 2.3 monomer? [388]; A369D mutant; 1 Ca, 4 NAGs, 5 MANs, and 89 HOHs; 9 SSs #6nn9 2.3 monomer? [388]; K432N mutant; 1 Ca, 4 NAGs, 5 MANs, and 87 HOHs; 9 SSs Neuraminidase N9-NC41 (Influenza virus A/Whale/Maine/1/84) (1ncd.N: 2nn9 [2bat] [1nsc.A]) {6 X 4 anti beta wheel + coil cap} #1ncd 2.9 monomer? + Fab dimer - 3 chains given [389, 214, 221]; 1 Ca++, 5 NAGs, 4 MANs, and 69 HOHs; 14 SSs Neuraminidase Sialidase (Influenza virus - strain B, Beijing 1/87) (1nsc.A: 1nsc.A [2nn9] [2bat]) {6 X 4 anti beta wheel + coil cap} #1nsb 2.2 tetramer - 2 chains given [390]; 2 NAGs, 3 Ca++s, 446 HOHs; 16 SSs #1nsc 1.7 tetramer - 2 chains given [390]; 2 NAGs, 2 sialic acids, 3 Ca++s, 506 HOHs; 16 SSs #1nsd 1.8 tetramer - 2 chains given [390]; 2 NAGs, 2 2,3-dehydro-2-deoxy- N-acetyl neuraminic acids, 3 Ca++s, 506 HOHs; 16 SSs Neuroglian (Drosophila melanogaster) {domain 1: 610-709: Greek anti beta} {domain 2: 710-814: Greek anti beta} #1cfb 2.0 fragment [205]; residues 610-814; 3 NAGs, 1 SO4, 1 Na+, and 237 HOHs; 1 SS Neurophysin II (Bos taurus) (1bn2.1: 1bn2.1) {SS rich c/b/b/ac back to back open face anti beta cr/cr} #1bn2 2.8 CA monomer + dipeptide (4a + 5p) - 9 chains given [95, 2]; 5 p-iodo- Phe-Tyr peptides; 28 SSs Neurotoxin, Variant 1 (Centruroides sculpturatus Ewing) (1vnb: 2sn3) {SS rich a/b open face anti beta} [sn3+] #1vna NMR monomer - 26 models given [65]; 4 SSs #1vnb NMR monomer [65]; minimized average structure; 4 SSs Alpha-Neurotoxin (Dendroapsis polylepsis polylepsis) (1ntx: 3ebx [1cdt.A] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich c/b/c doubly wound anti beta ud/ud + anti beta} [tox+] #1ntx NMR monomer? - 20 models given [60]; 4 SSs Neurotoxin I (Stichodactyla helianthus) (1sh1: 1sh1 [1atx]) {SS rich c/b/c doubly wound anti beta ud/cr} XXX Thornton ss rich beta #1sh1 NMR monomer [48]; energy minimized average structure; pH 5.0; 300K; 3 SSs #2sh1 NMR monomer - 8 models given [48]; pH 5.0; 300K; 3 SSs each Neurotoxin II (Naja naja oxiana) (1nor: 3ebx [1cdt.A] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich c/b/c doubly wound anti beta ud/ud + anti beta} [tox+] #1nor NMR monomer - 19 structures [61]; 4 SSs Neurotrophin #1bnd NMR dimer Neutral Protease (Bacillus cereus, strain DSM 3101) (1npc: 8tln [1ezm]) {domain 1: 1-127: a/b open face para beta + anti beta} {domain 2: 128-317: encircled axial alpha + anti beta + anti alphas} or {domain 1: 1-153: a/b/c doubly wound mixed beta ud/cr + anti beta} {domain 2: 154-317: a/a/a doubly wound para alpha ud/cr + anti betas + [tln+] XXX check #1npc 2.0 monomer? [317]; 4 Ca++s, 1 Zn++, and 304 HOHs Nicotinic Acetylcholine Receptor (Torpedo californica) (1abt.B: 1abt.B) {coil} DUP1abt NMR fragment + bungarotoxin - 4 models of 2 chains each [12, 74] Nitrate Reductase (Zea mays) {domain 1: 11-119: Greek anti beta + alpha cap} {domain 2: 120-270: a/b/a doubly wound para beta ud/ud + anti beta} #1cnd 2.5 fragment [270]; 1 FAD and 94 HOHs Nitrite Reductase (Achromobacter cycloclastes) {domain 1: 11-161: Greek anti beta + alpha} XXX {domain 2: 162-340: double stranded anti beta cylinder + anti beta + alphas} #1afn 2.6 trimer (a3) - 3 chains given [330]; 6 Cu++s and 34 HOHs Nitrite Reductase (Achromobacter cycloclastes) (1nrd: 1nrd) {domain 1: 8-160: Greek anti beta + c/b open face para beta + alphas} {domain 2: 161-340: double stranded anti beta cylinder + para beta + alphas} #1nrd 2.3 CA trimer - 1 chain given [333]; 2 Cus and 1 HOH Nitrogenase Iron Protein (Azotobacter vinelandii) (1nip.A: 1nip.A) {a/b/a doubly wound para beta ud/ud} #1nip 2.9 dimer (a2) - 2 chains given [289]; 2 Mg-4H2Os, 1 FS4, 1 ADP, and 9 HOHs Nitrogenase Molybdenum-Iron Protein (Azotobacter vinelandii) (1min.A: 1min.A [1mio.A]) {domain 1: A5-59,A347-490: a/b/a doubly wound para beta ud/ud + anti alpha} {domain 2: A60-206: a/b/a doubly wound para beta ud/ud} {domain 3: A207-346: a/b/a doubly wound para beta ud/ud+cr + anti alpha} (1min.B: 1min.B [1mio.B]) {domain 4: B2-67,B342-523: a/b/a doubly wound para beta ud/ud + para alpha + wedge alphas} {domain 5: B68-212: a/b/a doubly wound para beta ud/ud} {domain 6: B213-341: a/b/a doubly wound para beta ud/ud+cr} #1min 2.2 dimer? (2ab) - 4 chains given [492, 523]; 2 Ca++s, 2 3-hydroxy-3- carboxy-adipic acid, 2 Fe7-Mo1-S9 clusters, 2 Fe8-S8 clusters, and 4 HOHs Nitrogenase Molybdenum-Iron Protein (Clostridium pasteurianum) (1mio.A: 1mio.A [1min.A]) {domain 1: A2-50,A336-526: a/b/a doubly wound para beta ud/ud + anti alpha} {domain 2: A51-197: a/b/a doubly wound para beta ud/ud} {domain 3: A198-335: a/b/a doubly wound para beta ud/ud+cr + anti alpha} (1mio.B: 1mio.B [1min.B]) {domain 4: B2-161: a/b/a doubly wound para beta ud/ud + para alpha + wedge alphas} {domain 5: B162-289: a/b/a doubly wound para beta ud/ud} {domain 6: B290-458: a/b/a doubly wound para beta ud/ud+cr} #1mio 3.0 dimer? (2ab) - 4 chains given [533, 458]; 2 Ca++s, 2 3-hydroxy-3- carboxy-adipic acids, 2 Fe7-Mo1-S9 clusters, and 2 Fe8-S8 clusters Nucleoside Diphosphate Kinase (Dictostelium discoideum) (1ndk: 1ndk [2nck.L]) {a/b/a doubly wound anti beta ud/cr} #1ndk 2.2 hexamer (a6) - 1 chain given [155]; H122C mutant; 28 HOHs Nucleoside Diphosphate Kinase (Myxococcus xanthus) (2nck.L: 2nck.L [1ndk]) {a/b/a doubly wound anti beta ud/cr} #2nck 2.0 dimer? (a2) - 2 chains given [144]; tetragonal form; 205 HOHs Omega-AGA-IVB (Agelenopsis aperta) (1omb: 1omb) {SS rich c/b open face anti beta cr} #1oma NMR monomer - 21 models given [48]; 4 SSs #1omb NMR monomer [48]; minimized average structure; 4 SSs Oncomodulin (Rattus norvegicus) (1rro: 1rro [2sas] [4icb] [1osa] [4cpv] [1rec]) {crossed alpha + anti beta} XXX Thornton EF hand #1omd 1.85 monomer [108]; 3 Ca++s and 87 HOHs #1rro 1.3 monomer [108]; 4 Ca++s and 103 HOHs Orotate Phosphoribosyltransferase (Salmonella trypimurium) {a/b/a doubly wound para beta ud/cr + anti beta + anti alpha} XXX #1sto 2.6 monomer? [213]; 1 HYD, 1 orotidine 5'-monophosphate, and 77 HOHs Ovalbumin (Gallus domesticus) (1ova.A: 1ova.A [2ach.A] [7api.A] [1pai.A] [1hle.A] [1hle.B]) {domain 1: 23-53,193-290,344-391: a/b open face anti beta ud + anti beta + alpha} {domain 2: 54-192,291-343: a/b/a doubly wound mixed beta ud/ud + alpha} #1ova 1.95 monomer - 4 chains given [386]; 3 phosphoryl groups, 4 NAGs, 1 Ca, and 678 HOHs; 3 SSs Ovomucoid Third Domain (Coturnix coturnix japonica) (3ovo: 2ovo [1hpt] [3sgb.I] [2bus]) {SS rich a/b open face anti beta ud + coil} XXX [inhibit] #1ovo 1.9 monomer, but crystallographically an octamer (a8) - 4 chains given [56]; part of protein; 46 HOHs; 12 SSs #3ovo 1.55 monomer [56]; part of protein; 34 HOHs; 3 SSs Ovomucoid Third Domain (Meleagris gallopavo) (3sgb.I: 3sgb.I [2ovo] [1hpt] [2bus]) {SS rich a/b open face anti beta ud} [inhibit] XXX Thornton beta open sandwich2 DUP1cho 1.8 ovomucoid inhibitor + proteinase - 2 chains given [56, 245]; 221 HOHs DUP1ppf 1.8 ovomucoid inhibitor + proteinase - 2 chains given [56, 218]; 6 NAGs, 2 FUCs, 6 MANs, 2 GLCs, and 272 HOHs; 7 SSs DUP3sgb 1.8 ovomucoid inhibitor + proteinase - 2 chains [56, 185]; supersedes 2sgb; 182 HOHs Ovomucoid Third Domain (Lophura nycthemera) (2ovo: 2ovo [1hpt] [3sgb.I] [2bus]) {SS rich a/b open face anti beta ud} [inhibit] XXX Thornton beta open sandwich2 #2ovo 1.5 monomer [56]; part of protein; 31 HOHs; 3 SSs #4ovo 2.50 monomer [56]; part of protein; 25 HOHs; 3 SSs Ovotransferrin (Duck) (1ovb: 1ovb [1lfg]) {a/b/a doubly wound anti beta ud/ud + anti beta + alpha} #1ovb 2.3 fragment [159]; domain II from N-terminal lobe; Fe+++, 1 car- bonate, and 106 HOHs; 4 SSs 1-Beta-Mercaptopropionate Oxytocin (synthetic) (1xy1.A: 1xy1.A) {SS rich coil} #1xy1 1.04 monomer - 2 chains given [8]; wet form; N termini - 2 beta- mercaptopropionates, 2 terminal amides, and 13 HOHs; 2 SSs #1xy2 1.20 monomer [8]; dry form; N terminus - 1 beta-mercaptopropionate, 1 terminal amide, and 7 HOHs; 1 SS P22 C2 Repressor (Salmonella bacteriophage P22) (1adr: 1adr) {a/a/a doubly wound para alpha cr/cr} #1adr NMR monomer - 20 models given [76]; N-terminal DNA-binding domain P-30 Protein (Rana pipiens) (1onc: 1onc) {domain 1: 1-38,61-85: SS rich a/b open face anti beta cr + alpha} {domain 2: 39-60,86-104: SS rich a/c open face anti alpha cr} XXX #1onc 1.7 monomer [104]; 1 SO4 and 97 HOHs; 4 SSs Avian Pancreatic Polypeptide (Meleagris gallopavo) (1ppt: 1ppt [1bba]) {alpha + coil} #1ppt 1.37 dimer (a2) - 1 chain given [36]; 1 Zn++ Pancreatic Polypeptide (Bos taurus) (1bba: 1bba [1ppt]) {alpha + coil} #1bba NMR monomer [36]; mean structure Pancreatic Secretory Trypsin Inhibitor (Sus scrofa) (1tgs.I: 1hpt [2ovo] [3sgb.I] [2bus]) {SS rich a/b open face anti beta ud} XXX [inhibit] XXX Thornton beta open sandwich2 DUP1tgs 1.8 monomer + trypsinogen protease - 2 chains [56, 229]; 1 Ca++, 1 SO4, and 152 HOHs; 9 SSs Pancreatic Secretory Trypsin Inhibitor (Homo sapiens, transduced in E. coli) (1cgi.I: 1hpt [2ovo] [3sgb.I] [2bus]) {SS rich a/b open face anti beta ud} DUP1cgi 2.3 inhibitor + chymotrypsinogen - 2 chains given [56, 245]; variant 3 (18Y); 52 HOHs; 8 SSs DUP1cgj 2.3 inhibitor + chymotrypsinogen - 2 chains given [56, 2456]; variant 4 (18L); 56 HOHs; 8 SSs #1hpt 2.3 monomer [56]; variant 3 (18Y); 31 HOHs; 3 SSs Pancreatic Spasmolytic Polypeptide (Sus scrofa) (1pos.A: 1pos.A) {SS rich coil} XXX #1pos 2.6 CA monomer - 2 chains given [106] Panleukopenia Viral Protein 2 (Felis domestica virus, Strain B) (1fpv: 2cas) {multiple anti beta} XXX #1fpv 3.3 60mer [584]; empty particles; icosahedral; 1 SS Papain (Carica papaya) (9pap: 9pap [2act]) {domain 1: 1-18,113-206: up down anti beta + alpha caps} XXX {domain 2: 19-112: schief alpha + anti beta + coil} [pap] #1pad 2.8 monomer + inhibitor - 2 chains given [212, 5]; inhibitor: acetyl- ala-ala-phe-alm derivative of C25; supersedes 2pap; based on 8pap; 32 HOHs; 3 SSs #2pad 2.8 monomer + substrate - 2 chains given [212, 1]; cysteinyl deriva- tive of C25; based on 8pap; supersedes 3pap; 30 HOHs; 3 SSs #4pad 2.8 monomer [212]; tosyl-methylenyllysyl derivative of C25; based on 8pap; supersedes 5pap; 1 para-toluene sulfonate, 1 lysine, -methylene C bound to carboxy C, and 30 HOHs; 3 SSs #5pad 2.8 monomer + inhibitor - 2 chains [212, 4]; based on 8pap; super- sedes 6pap; 1 benzoyloxy residue bound to N of I:F2, 1 glycine- methylene C bound to carboxy C, 30 HOHs; 3 SSs #6pad 2.8 monomer + inhibitor - 2 chains [212, 3]; based on 8pap; super- sedes 7pap; 1 benzoyloxy residue bound to N of I:F2, 1 alanine- methylene C bound to carboxy C, and 30 HOHs; 3 SSs #9pap 1.65 monomer [212]; supersedes 3pad; Cys-25 oxidized; 29 methanols and 195 HOHs; 3 SSs #1pe6 2.1 monomer [204]; 1 E-64-C inhibitor, 14 methanols and 181 HOHs; 3 SSs #1pip 1.7 monomer + peptide - 2 chains given [212, 5]; peptide: succinyl- Gln-Val-Val-Ala-Ala-p-nitroanilide; 3 SSs #1pop 2.1 monomer + peptide - 2 chains given [212, 4]; peptide: N-acetyl- L-leucyl-L-leucyl-L-arginal covalently attached to C25; 24 meth- anols and 175 HOHs; 3 SSs #1ppd 2.0 monomer [212]; 2-hydroxyethylthiopapain; crystal form D; C25 in- hibited with bound 2-mercaptoethanol and 211 HOHs; 3 SSs #1ppn 1.61 monomer [212]; 1 O bound to Cys 25, 1 methanol, and 226 HOHs; 3 SSs #1ppp 1.9 monomer [212]; 1 (2S,3S)-3-(1-(N-(3-methylbutyl)amino)-leucylcar- boxyl)oxirane-2-carboxylate, 1 methanol, and 205 HOHs; 3 SSs #1stf 2.37 monomer + inhibitor (a + i) - 2 chains given [212, 98]; C:I8S mutant; 1 carboxymethyl group and 142 HOHs; 3 SSs PAPd Chaperone Protein (Escherichia coli) (3dpa: 3dpa) {domain 1: 1-121: Greek anti beta + alpha} {domain 2: 122-218: Greek anti beta + alpha} #3dpa 2.5 CA monomer [218] Papillomavirus-1 E2 (Papillomavirus-1) (2bop.A: 2bop.A) {a/b open face anti beta ud} #2bop 1.7 dimer + DNA (a2 + d2) - 2 chains given [85, 17]; DNA-binding domain, residues 325-410; 2 Ybs and 121 HOHs Parvalbumin (Esox lucius) (1pal: 4cpv [2sas] [4icb] [1osa] [1rro] [1rec]) {crossed alpha + anti beta + anti alpha pair} [ca_bind+] #1pal 1.65 monomer [108]; pI 4.10; 2 Ca++s, 1 ammonium ion, and 64 HOHs #2pal 1.8 monomer [108]; pI 4.10; 3 Mn++s and 62 HOHs #3pal 2.4 monomer [108]; pI 4.10; 2 Ca++s, 1 Mg++, and 95 HOHs #4pal 1.8 monomer [108]; pI 4.10; 2 Mg++s, 1 Ca++, and 88 HOHs Alpha-Parvalbumin (Rattus rattus) (1rtp.1: 4cpv [2sas] [4icb] [1osa] [1rro] [1rec]) {crossed alpha + anti beta + anti alpha pair} [ca_bind+] #1rtp 2.0 monomer? - 3 chains given [109]; 6 Ca++s and 110 HOHs Parvalbumin Alpha (Triakis semifasciata) (5pal: 4cpv [2sas] [4icb] [1osa] [1rro] [1rec]) {crossed alpha + anti beta + anti alpha pair} [ca_bind+] #5pal 1.54 monomer [109]; 2 Ca++s and 92 HOHs PDC-109 (Bos taurus) (1pdc: 1pdc) {SS rich b/b open face anti beta} XXX #1pdc NMR monomer? [45]; domain B; best structure; 2 SSs Pectate Lyase C (Erwinia chrysanthemi EC16) (1pec: 1pec) {singly wound para beta cylinder} #1pec 2.2 CA monomer? [353]; 2 SSs Pepsin (Mucor pusillus) (1mpp: 1mpp [3psg] [1smr.A] [1lya.B] [2apr]) {domain 1: multiple anti beta} [ac_prot+] XXX {domain 2: multiple anti beta} [ac_prot+] #1mpp 2.0 monomer? [361]; 1 SO4 and 221 HOHs; 2 SSs Pepsin (Sus scrofa) (3psg: 3psg [1smr.A] [1lya.B] [1mpp] [2apr]) {domain 1: 1-174?: multiple anti beta} [ac_prot] XXX {domain 2: 175?-326: multiple anti beta} [ac_prot] XXX Thornton twisted sheet #3pep 2.3 monomer [326]; 2 ethanols and 206 HOHs; 3 SSs #4pep 1.8 monomer [326]; supersedes 1pep; 1 phosphate and 187 HOHs; 3 SSs #5pep 2.34 monomer [326]; supersedes 2pep; 371 HOHs; 2 residues differ from 3pep, 4pep, and 3psg; 3 SSs #1psa 2.9 monomer + peptide (a + i) - 4 chains given [370, 4]; zymogen; 2 ethoxycarbonyls, 2 cyclohexylmethyl-2,3,-dihydroxy-5-methyl- hexylamide, and 110 HOHs; 6 SSs #2psg 1.8 monomer [370]; zymogen; 3 phosphoryls and 237 HOHs; 3 SSs #3psg 1.65 monomer [370]; zymogen; supersedes 1psg; 180 HOHs Peroxidase (Arthromyces ramosus) (1arp: 1arp [1lga.A]) {domain 1: 9-152,283-302: schief anti alpha 4 helix bundle + alpha} XXX {domain 2: 153-282,303-344: encircled axial alpha + coil} #1arp 1.9 monomer? [344]; 1 HEM with Fe++, 2 Ca++s, 2 NAGs, and 246 HOHs; 4 SSs PKI (?) (2cpk.I: 1apm.I) {alpha + coil} DUP1apm 2.0 fragment + catalytic subunit [20, 350]; S139A mutant; 3 residues are phosphorylated; n-octane and 207 HOHs DUP1atp 2.2 fragment + catalytic subunit [20, 350]; 2 residues are phos- phorylated; ATP, 2 Mn++s, and 103 HOHs DUP2cpk 2.7 fragment + catalytic subunit [20, 350]; supersedes 1cpk; 3 resi- dues are phosphorylated DUP1ctp 2.9 fragment + catalytic subunit [20, 350]; 1 myristate, 1 phos- phoryl group, 2 Is, and 2 HOHs Phaseolin (Phaseolus vulgaris) (1phs: 1phs [1cau.A] [1cau.B]) {domain 1: 11-21,39-49,220-381: double stranded anti beta cylinder + anti alpha + alpha} {domain 2: 22-38,50-212: double stranded anti beta cylinder + anti alpha + alpha} #1phs 3.0 CA dodecamer (4a3]) [397]; crystallizes as tetramer of trimers Pheromone ER-1 (Euplotes raikovi) {up down anti alpha 3 helix bundle} #1erc NMR monomer? - 20 models given [40]; 3 SSs Pheromone ER-2 (Euplotes raikovi) {up down anti alpha 3 helix bundle} #1erc NMR monomer? - 20 models given [40]; 3 SSs Pheromone ER-10 (Euplotes raikovi) (1erp: 1erp) {up down anti alpha 3 helix bundle} #1erp NMR monomer? - 20 models given [38]; 3 SSs Phosphate Binding Protein (Escherichia coli) (1abh: 1abh) {domain 1: 1-80,210-322: a/b misc beta} XXX {domain 2: 81-209: a/b misc beta} XXX #1abh 1.7 CA monomer? [321]; 1 phosphate Phosphatidylinositol 3-Kinase (Bos taurus) (2pnb: 2pnb) {a/b/a doubly wound para beta ud/ud + anti alpha} (1pnj: 1pnj) {Greek anti beta} XXX #2pna NMR fragment - 22 models given [104]; N-terminal SH2 domain of P85- alpha subunit #2pnb NMR fragment [104]; N-terminal SH2 domain of P85-alpha subunit; mini- mized average structure #1pnj NMR fragment [86]; alpha subunit, SH3 domain; minimized average structure #2pni NMR fragment - 26 models given [86]; P85-alpha subunit, SH3 domain Phosphocarrier III GLC tFast (Escherichia coli) (1f3g: 1f3g [1gpr]) {domain 1: 19-55,136-168: Greek anti beta + alpha} {domain 2: 56-135: Greek anti beta + alpha} #1f3g 2.1 monomer [161]; 22 HOHs DUP1gla 2.6 monomer + glycerol kinase tetramer (4a + b4) - 2 chains given [168, 501]; 1 glycerol DUP1glb 2.6 monomer + glycerol kinase tetramer (4a + b4) - 2 chains given [168, 501]; 1 glycerol and 1 ADP DUP1glc 2.65 monomer + glycerol kinase tetramer (4a + b4) - 2 chains given [168, 501]; 1 G3P, 1 ADP, 1 Mg++, 1 Zn++, and 42 HOHs DUP1gld 2.93 monomer + glycerol kinase tetramer (4a + b4) - 2 chains given [168, 501]; 1 G3P, 1 ADP, 1 Mn++, and 17 HOHs DUP1gle 2.94 monomer + glycerol kinase tetramer (4a + b4) - 2 chains given [168, 501]; 1 G3P, 1 ADP, 2 Zn++s, and 48 HOHs Phosphofructokinase (Bacillus stearothermophilus) (3pfk: 1pfk.A) {domain 1: 1-138,252-320: a/b/a doubly wound para beta ud/ud + a/b open face anti beta ud + alpha} {domain 2: 139-251: a/b/a doubly wound para beta ud/ud} [kinase] #3pfk 2.4 tetramer (a4) - 1 chain given [319]; unliganded; 2 phosphates and 91 HOHs #4pfk 2.4 tetramer (a4) - 1 chain given [319]; 1 F6P, 2 ADPs, 2 Mg++s, and 70 HOHs #5pfk 7.0 CA tetramer (a4) - 1 chain given [319]; inhibitor 2-phosphoglycolate Phosphofructokinase (Escherichia coli) (1pfk.A: 1pfk.A) {domain 1: 0-138,252-319: a/b/a doubly wound para beta ud/ud + a/b open face anti beta ud + alpha} {domain 2: 139-251: a/b/a doubly wound para beta ud/ud} [kinase] #1pfk 2.4 tetramer (a4) - 2 chains given [320]; 2 FBPs, 4 ADPs, 4 Mg++s and 277 HOHs #2pfk 2.4 tetramer (2ab?) - 4 chains given, but 2 are part of one tetramer & the other two are part of another [320]; chains A and B differ from chains C and D; unliganded; 347 HOHs Phosphoglucomutase (Lepus cuniculus) (2pmg.A: 2pmg.A) {domain 1: 1-218: a/b/a doubly wound mixed beta ud/ud + anti beta + wedge alpha} {domain 2: 219-302,390-420: a/b/a doubly wound mixed beta ud/ud + alpha} {domain 3: 303-389: a/b/a doubly wound mixed beta ud/ud} {domain 4: 421-561: a/b open face mixed beta cr} #2pmg 2.7 monomer? - 2 chains given [561] 6-Phosphogluconate Dehydrogenase (Ovis orientalis aries) (1pgd: 1pgd) {domain 1: 1-160: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/ud} {domain 2: 161-469: a/a/a doubly wound anti alpha cr/cr} XXX #1pgd 2.5 dimer (a2) - 1 chain given [482]; 1 SO4 and 61 HOHs Phosphoglycerate Kinase (Equus caballus) (2pgk: ???) {domain 1: 0-188,397-407: a/b/a doubly wound para beta ud/ud + anti beta} {domain 2: 189-396: a/b/a doubly wound para beta ud/ud + anti beta} [pgk] #2pgk 3.0 monomer? [407]; all residues UNK Phosphoglycerate Kinase (Saccharomyces cerevisiae) (3pgk: 3pgk) {domain 1: 0-197,402-415: a/b/a doubly wound para beta ud/ud + anti beta + alpha wedge} {domain 2: 198-401 a/b/a doubly wound para beta ud/ud + crossed alpha [pgk] #3pgk 2.5 monomer [416]; supersedes 1pgk; 1 ATP, 1 Mg++, and 1 3-phospho- glycerate Phosphoglycerate Mutase (Saccharomyces cerevisiae) (3pgm: 3pgm) {a/b/a doubly wound para beta ud/ud + coil + wedge alpha} [pgm] #3pgm 2.8 tetramer (a4) - 1 chain given [241]; supersedes 1pgm; 1 3-phos- phoglycerate and 2 SO4s Phospholipase A2 (Agkistrodon piscivorus piscivorus) (1ppa: 1ppa [1poa] [1pod] [1pp2.L]) {a+b greek key + wedge alpha + coil} [plipase+] #1ppa 2.0 monomer [121]; Lys 49 variant; 1 aniline and 151 HOHs; 7 SSs Phospholipase A2 (Apis mellifera) (1poc: 1poc) {domain 1: 1-38,61-92: SS rich up down anti alpha 3 helix bundle} XXX {domain 2: 39-60,93-134: SS rich Greek anti beta} XXX #1poc 2.0 monomer? [134]; complex with transition-state analogue; 1 L-1- O-octyl-2-heptyl-phosphonyl-sn-glycero-3-phospho-ethanolamine, 1 Ca++, and 80 HOHs; 5 SSs Phospholipase A2 (Bos taurus l.) (4bp2: 1poa [1pod] [1pp2.L] [1ppa]) {a+b greek key + wedge alpha + coil} [plipase] #1bp2 1.7 monomer [123]; 1 Ca++, 2 2-methyl-2,4-pentanediols, 106 HOHs; 7 SSs #2bp2 3.0 monomer [130]; zymogen, with 7 res leader; coordinates for the leader peptide are not included; 7 SSs #3bp2 2.1 monomer [123]; transaminated; 1 Ca++, 1 pyruvoyl group, and 86 HOHs; 7 SSs #4bp2 1.6 monomer [130]; zymogen, with 4 res leader, not seen in density; 1 Ca++, 2 2-methyl-2,4-pentanediols, and 60 HOHs; 7 SSs #2bpp 1.8 monomer [123]; cloned gene; 1 Ca++; 7 SSs #1bpq 1.8 monomer [123]; K56M mutant; 1 Ca++; 7 SSs Phospholipase A2 (Crotalus atrox) (1pp2.L: 1pp2.L [1poa] [1pod] [1ppa]) {a+b greek key + wedge alpha + coil} [plipase] #1pp2 2.5 dimer (a2) - 2 chains given [122]; 137 HOHs; 14 SSs Phospholipase A2 (Homo sapiens) (1pod: 1pod [1poa] [1pp2.L] [1ppa]) {a+b greek key + alpha + anti beta + coil} [plipase+] #1bbc 2.2 monomer? [124]; 87 HOHs; 7 SSs #1pod 2.1 monomer? [124]; 1 Ca++ and 153 HOHs; 7 SSs #1poe 2.1 monomer? - 2 chains given [124]; transition-state analogue complex; 2 L-1-O-octyl-2-heptyl-phosphonyl-sn-gycero-3-phospho- ethanolamines, 4 Ca++s, and 314 HOHs; 13 SSs Phospholipase A2 (Sus Scrofa) (4p2p: 1poa [1pod] [1pp2.L] [1ppa]) {a+b greek key + wedge alpha + coil} [plipase] #1p2p 2.6 monomer [124]; 2 Ca++s and 5 HOHs; 7 SSs #3p2p 2.1 monomer - 2 chains given [119]; D59S, S60G, DEL(62-66), N67Y mutant; 3 Ca++s and 205 HOHs; 14 SSs #4p2p 2.4 monomer [124]; independent refinement of 1p2p data; 2 Ca++s and 8 HOHs; 7 SSs #5p2p 2.4 monomer - 2 chains given [119]; W3F, L31W, D59S, S60G, DEL(62- 66), N67Y mutant; 3 Ca++s, 2 R-dodecanoyl-amino-hexanol-phospho- glycols, and 126 HOHs; 14 SSs #2phi 2.2 monomer - 2 chains given [124]; F63V mutant; 3 Ca++s and 195 HOHs; 14 SSs Phospholipase A2 (Naja naja atra) (1poa: 1poa [1pod] [1pp2.L] [1ppa]) {a+b greek key + alpha + anti beta + coil} [plipase+] #1poa 1.5 monomer? [118]; 2 Ca++s and 151 HOHs; 7 SSs #1pob 2.0 monomer? - 2 chains given [118]; transition-state analogue complex; 2 L-1-O-octyl-2-heptyl-phosphonyl-sn-gycero-3-phospho- ethanolamines, 4 Ca++s, and 242 HOHs; 13 SSs Phospholipase A2 (Naja naja naja) (1psh.A: 1poa [1pod] [1pp2.L] [1ppa]) {a+b greek key + alpha + anti beta + coil} [plipase+] #1psh 2.3 monomer - 3 chains given [119]; 3 Ca++s and 148 HOHs; 21 SSs Phospholipase C-gamma (Homo sapiens) (1hsp: 1hsp [1shg] [1shf.A]) {Greek anti beta} XXX #1hsp NMR monomer? - 11 models given [71]; SH3 domain; model 0 is minimized mean structure N-(5' Phosphorybosyl) Anthranilate Isomerase : Indol-3-glycerol-phosphate Synthase (Escherichia coli) (1pii: 1pii) {domain 1: 1-254: a/b singly wound para beta + wedge alpha} [barrel+] {domain 2: 255-452: ac/b singly wound para beta} [barrel+] #1pii 2.0 monomer [452]; 2 phosphates and HOHs Phosphoribosylglycinamide Formyltransferase or Glycinamide Ribonucleotide Transformylase (Escherichia coli K12) (1cde: 1cde) {domain 1: 1-103: a/b/a doubly wound para beta ud/ud} {domain 2: 104-209: a/b open face anti beta ud + anti beta + alpha} #1cdd 2.8 monomer - 2 chains given [212]; apo; 2 phosphates #1cde 2.5 monomer [212]; holo; 1 glycinamide ribonucleotide and 1 5-deaza-5,6,7,8-tetrahydrofolate #1grc 3.0 dimer (a2) - 2 chains given [212]; 2 phosphates Phosphotransferase (Escherichia coli, Strain HPR) (1poh: 1poh [1ptf]) {a/b open face anti beta ud + alpha} #1poh 2.0 monomer? [85]; 2 SO4s and 89 HOHs Photoactive Yellow Protein (Ectothiorhodospira halophila) (1phy: 1phy) {crossed up down anti betas} #1phy 2.4 CA monomer? - 1 chain [126] XXX Photosynthetic Reaction Center (Rhodobacter sphaeroides, R-26) (4rcr.H: 4rcr.H [1prc.H]) {domain 1: alpha + anti beta} {domain 2: alpha + coil} {domain 3: misc anti beta} [prc-2+] (4rcr.L: 1prc.L [1prc.M] [4rcr.M]) {up down anti alpha} [prc-3+] (4rcr.M: 4rcr.M [1prc.L] [1prc.M]) {up down anti alpha} [prc-4+] #2rcr 3.1 trimer (abc) - 3 chains given [282, 308, 260]; membrane protein; 4 bacteriochlorophyll As, 2 bacteriopheophytin As, 1 Fe++, and 2 ubiquinone-10s; different depositor from 4rcr #4rcr 2.8 trimer (abc) - 3 chains given [281, 307, 260]; membrane protein; 4 bacteriochlorophyll As, 2 pacteriopheophytin As, 1 Fe++, 2 ubi- quinone-10s, 1 b-octylglucoside; different depositor from 2rcr Photosynthetic Reaction Center (Rhodopseudomonas viridis) (1prc.C: 1prc.C) {misc alpha} [prc-1] (1prc.H: 1prc.H [4rcr.H]) {domain 1: alpha + anti beta} {domain 2: alpha + coil} {domain 3: misc anti beta} [prc-2] (1prc.L: 1prc.L [1prc.M] [4rcr.M]) {up down anti alpha} [prc-3] (1prc.M: 1prc.M [1prc.L] [4rcr.M]) {up down anti alpha} [prc-4] #1prc 2.3 tetramer (abcd) - 4 chains given [336, 273, 323, + 259]; membrane protein; 4 bacteriochlorophyll Bs, 2 bacteriopheophytin Bs, 1 Fe++, 1 menaquinone-7, 4 HEMs with Fe++, 1 dihydroneurosporene, 1 ubiquinone-1, 2 lauryl dimethylamineoxides, 7 SO4s, and 201 HOHs Phthalate Dioxygenase Reductase (Pseudomonas cepacia DB01) (2pia: 2pia) {domain 1: 1-106: Greek anti beta} {domain 2: 107-223: a/b/a doubly wound para beta + 2 crossed alpha} {domain 3: 224-321: open face anti beta + alpha} #2pia 2.0 monomer? [321]; 1 FMN, 1 Fe2/S2 cluster, and 136 HOHs C-Phycocyanin (Fremyella diplosiphon) (1cpc.A: 1cpc.A [1cpc.B]) {up down anti alpha + crossed alpha} (1cpc.B: 1cpc.B [1cpc.A]) {up down anti alpha + crossed alpha} #1cpc 1.66 dodecamer (6ab) - 4 chains given [162, 172]; chains B and L have 1 residue different; 6 phycocyanobilins, 2 methyls for gamma-N-methyl asparagines, and 243 HOHs Pilin (Pseudomonas aeruginosa, Strain K) (1pak: 1pak) {SS rich coil} #1paj NMR fragment - 12 models given [18]; residues 128-144; 1 HYD; 1 SS #1pak NMR fragment [18]; average structure; residues 128-144; 1 HYD; 1 SS Tissue Plasminogen Activator T-PA Kringle 2 (Homo sapiens) (1tpk.A: 1tpk.A [1kdu] [1pk4] [2hpp.P] [2pf1]) {SS rich anti beta + alpha} #1pk2 NMR fragment [90]; Kringle 2 domain; best structure; 1 6-amino-hex- anoic acid; 3 SSs #1tpk 2.4 monomer (a3) - 3 chains given [88]; DEL1-2; 3 Cl's and 91 HOHs; 9 SSs Tissue-Like Plasminogen Activator Type 1, F1 (Homo sapiens) (1tpm: 1tpm) {SS rich up down anti beta} #1tpm NMR monomer [50]; minimized average structure; 2 SSs #1tpn NMR monomer - 28 models given [50]; 2 SSs Plasminogen Activator, Urokinase-Type (Homo sapiens) (1kdu: 1kdu [1tpk.A] [1pk4] [2hpp.P] [2pf1]) {SS rich anti beta + alpha} #1kdu NMR fragment [85]; kringle domain; minimized average structure; 3 SSs Plasminogen Kringle 1 (Homo sapiens) (1pkr: 1pk4 [1kdu] [1tpk.A] [2hpp.P] [2pf1]) {SS rich anti beta} #1pkr 2.48 fragment [82]; 2 Cl-s and 71 HOHs; 3 SSs Plasminogen Kringle 4 (Homo sapiens) (1pk4: 1pk4 [1kdu] [1tpk.A] [2hpp.P] [2pf1]) {SS rich anti beta} #1pk4 1.9 monomer [79]; 1 SO4 and 96 HOHs; 3 SSs #2pk4 2.25 monomer [80]; 16-aminohexanoic acid and 106 HOHs; 3 SSs Plastocyanin (Chlamydomonas reinhardtii) (2plt: 1plc [1aaj] [1paz]) {Greek anti beta} [plasto+] #2plt 1.5 monomer [98]; 1 Cu++, 1 Ca++, and 81 HOHs Plastocyanin (Enteromorpha prolifera) (7pcy: 1plc [1aaj] [1paz]) {Greek anti beta} [plasto] #7pcy 1.8 monomer [98]; 1 Cu and 105 HOHs Plastocyanin (Phaseolus vulgaris) (9pcy: 1plc [1aaj] [1paz]) {Greek anti beta} [plasto+] #9pcy NMR monomer - 16 models given [99]; reduced form; 1 Cu++ Plastocyanin (Populus nigra variant italica) (1plc: 1plc [1aaj] [1paz]) {Greek anti beta} [plasto] XXX Thornton Greek 2 #2pcy 1.8 monomer [99]; apo; pH 6.0; 42 HOHs #3pcy 1.9 monomer [99]; 1 Hg++ and 59 HOHs #4pcy 2.15 monomer [99]; pH 7.8; crosslinked with glutaraldehyde; 1 Cu+ and 34 HOHs #5pcy 1.80 monomer [99]; pH 7.0; 1 Cu+ and 44 HOHs #6pcy 1.90 monomer [99]; pH 3.8; 1 Cu+ and 48 HOHs #1plc 1.33 monomer [99]; supersedes 1pcy; pH 6.0; 1 Cu++ and 110 HOHs #1pnc 1.6 monomer [99]; PROLSQ refinement; 1 Cu++ and 189 HOHs #1pnd 1.6 monomer [99]; EREF refinement; 1 Cu++ and 171 HOHs Platelet Factor 4 (Bos taurus) (1plf.A: 1plf.A [1mca.A] [3il8]) {SS rich anti beta + alpha} #1plf 2.2 tetramer (a4) - 4 chains given [72]; 1 tetracyanonickelate anion (Ni(CN)4 --) and 79 HOHs; 8 SSs Platelet-Derived Growth Factor BB (Homo sapiens) (1pdg.A: 1pdg.A) {SS rich anti beta} #1pdg 3.0 dimer (a2) - 3 chains given [109]; 11 SSs Poliovirus, Type I, Mahoney Strain (Homo sapiens) (2plv.1: 2plv.1 [4rhv.1] [1r1a.1]) {Greek anti beta} [virus] XXX Thornton Jelly Roll (2plv.2: 2plv.2 [1bbt.2] [1tme.2]) {Greek anti beta} [virus] (2plv.3: 2plv.3 [1bbt.3] [4rhv.3] [1tme.3]) {Greek anti beta} [virus] (2plv.4: 2plv.4) {coil + anti beta + alpha} #2plv 2.88 240mer (60abcd) - 4 chains given [302, 272, 238, 69]; 1 myri- state, 1 sphingosine, and 479 HOHs Polymerase III (Escherichia coli) (2pol.A: 2pol.A) {domain 1: open face anti beta + alpha} XXX {domain 2: open face anti beta + alpha} {domain 3: open face anti beta + alpha} {domain 4: open face anti beta + alpha} #2pol 2.5 dimer? - 2 chains given [366]; beta subunit; 150 HOHs XXX Polypeptide Chymotrypsin Inhibitor PCI-1 (Solanum suberosum) (4sgb.I: 4sgb.I) {SS rich c/b open face anti beta cr} DUP4sgb 2.1 monomer + proteinase B - 2 chains [51, 185] ; 1 Ca++, 2 SO4s, and 179 HOHs Matrix Porin (Escherichia coli) (1omf: 1omf) {up down anti beta + alpha/coil interior loop + anti beta} #1omf 2.4 trimer? - 1 chain given [340]; membrane protein Phosphoporin (Escherichia coli) (1pho: 1omf) {up down anti beta + alpha/coil interior loop} #1pho 3.0 trimer? - 1 chain given [330]; membrane protein Porin (Rhodobacter capsulatus) (2por: 2por) {up down anti beta + alpha/coil interior loop + alpha} *good for structure picture #2por 1.8 trimer (a3) - 1 chain given [301]; membrane protein; 3 Ca++s, 4 N-octyltetraoxyethylenes, and 274 "HOHs" #3por 2.5 trimer (a3) - 1 chain given [301]; membrane protein; crystal form A'; 1 N-octyltetraoxyethylene, 1 TRIS(hydroxymethyl)-amino- methane, and 77 "HOHs" Porphobilinogen Deaminase (Escherichia coli) (1pda: 1pda) {domain 1: 3-101,195-221: a/b/a doubly wound para beta ud/ud + a/b open face anti beta cr} {domain 2: 102-194: a/b/a doubly wound para beta ud/ud + a/b open face anti beta cr} {domain 3: 222-307: a/b open face anti beta cr} #1pda 1.76 monomer? [313]; 1 dipyrromethane covalently attached to C242, 1 acetate, and 249 HOHs Profilin I (Acanthamoeba castellanii) {a/b/a+b doubly wound anti beta ud/cr} #1acf 2.0 monomer? [125]; 64 HOHs Achromobacter Protease I (Achromobacter lyticus M497-1) (1arb: 1arb) {domain 1: 1-133,230-263: Greek anti beta + alpha} {domain 2: 134-229: Greek anti beta} [s_prot+] #1arb 1.2 monomer? [268]; 153 HOHs; 3 SSs #1arc 2.0 monomer? [268]; 1 N-alpha-P-tosyl-L-lysine chloromethyl ketone and 72 HOHs; 3 SSs Protease Omega (Carica papaya) (1ppo: 9pap [2act]) {domain 1: 1-10,111-218: c/b open face anti beta + alpha caps + anti beta} lrdudl with alpha caps {domain 2: 11-110: crossed alpha} [pap] XXX check #1ppo 1.8 monomer [216]; 1 Cys 25 with Hg++ and 133 HOHs; 3 SSs Protein A (Staphylococcus aureus) (1fc2.C: 1fc2.C) {c/a open face anti alpha ud} DUP1fc2 2.8 monomer + antibody dimer (a2) - 2 chains given [58, 224]; frag- ment B only; half of Ig given; 1 FUC, 1 GAL, 3 MANs, 4 NAGs, and 1 SO4 Protein C Inhibitor (Homo sapiens) (1pai.A: 1pai.A [1ova.A] [2ach.A] [7api.A] [1hle.A] [1hle.B]) (1pai.B: 1pai.B [2ach.B] [7api.B]) {domain 1: 5-53,194-289,359-391: a/b/b doubly wound anti beta cr/cr + alpha} {domain 2: 54-193,290-358: a/b/a doubly wound anti beta ud/ud} #1pai --- monomer (cleaved) - 2 chains given [354, 33]; model 1 #2pai --- monomer (cleaved) - 2 chains given [354, 33]; model 2 Protein G (Streptococcus Lancefield Group G and Streptococcus strain GX7805) (1pgx: 1pgx) {domain B2+2igh: a/b open face anti beta cr} {domain 2igg: a/b open face anti beta cr} #2igg NMR monomer? - 27 models given [64]; 2nd IgG-binding domain #2igh NMR monomer? - 24 models given [61]; 3rd IgG-binding domain; subset of 1pgx sequence #1pgx 1.66 monomer? [83]; B2 domain; 59 HOHs Protein G (Streptomyces griseus) (2gb1: 1pgx) {a/b open face anti beta cr} XXX Thornton twisted beta 2 #1gb1 NMR monomer - 60 models given [56]; B1 domain #2gb1 NMR monomer [56]; B1 domain; restrained minimized average structure Proteinase A (Streptomyces griseus, strain K1) (2sga: 2sga [2alp]) {domain 1: 1-133,230-263: Greek anti beta + alpha} {domain 2: 134-229: Greek anti beta} [s_prot] XXX Thornton Greek #2sga 1.5 monomer [181]; supersedes 1sga; 220 HOHs; 2 SSs #3sga 1.8 monomer + ace-PAPF-aldehyde inhibitor - 2 chains given [181, 5]; 1 phenylalaninal and 191 HOHs; 2 SSs #4sga 1.8 monomer + ace-PAPF inhibitor - 2 chains [181, 5]; 184 HOHs; 2 SSs #5sga 1.8 monomer + ace-PAPY inhibitor - 2 chains [181, 5]; 1 Na+ and 185 HOHs; 2 SSs #1sgc 1.8 monomer [181]; 1 chymostatin A; 2 SSs Proteinase B (Streptomyces griseus, strain K1) (3sgb.E: 2sga [2alp]) {domain 1: 1-133,230-263: Greek anti beta + alpha} {domain 2: 134-229: Greek anti beta} [s_prot] #3sgb 1.8 monomer + ovomucoid inhibitor - 2 chains [185, 56]; supersedes 2sgb; 182 HOHs; 5 SSs #4sgb 2.1 monomer + potato inhibitor - 2 chains [185, 51]; 1 Ca++, 2 sul- fates, and 179 HOHs Proteinase K (Tritirachium album limber) (2pkc: 2pkc [1thm] [1cse.E]) {a/b/a doubly wound para beta ud/ud + a/b open face anti beta ud + anti beta} [sbt] #1pek 2.2 monomer + peptides - 3 chains given [279, 4, 2]; 188 HOHs; 2 SSs #2pkc 1.5 monomer [279]; 1 Na+ and 194 HOHs; 2 SSs #2prk 1.5 monomer [279]; pseudodimer in crystal; 2 Ca++s and 178 HOHs; 2 SSs #3prk 2.2 monomer + inhibitor - 2 chains given [279, 4]; 1 methoxysuccinyl group, 1 methylene, 1 Ca++, and HOHs; 2 SSs #1ptk 2.4 monomer [279]; 2 Hg++s, 1 Ca++, and 198 HOHs; 2 SSs Proteinase Inhibitor IIA (Bos taurus) (2bus: 2bus [2ovo] [1hpt] [3sgb.I]) {SS rich a/b open face anti beta ud} #1bus NMR monomer - 5 models given [57]; 3 SSs #2bus NMR monomer [57]; energy minimized structure; 3 SSs Protocatechuate 3,4-Dioxygenase (Pseudomonas aeruginosa) (1pcd.A: 1pcd.A [1pcd.B]) {Greek anti beta + wedge alphas} (1pcd.B: 1pcd.B [1pcd.A]) {Greek anti beta + wedge alphas} #1pcd 2.8 CA dimer? - 2 chains given [200, 237]; 1 Fe; XXX obsolete Pseudoazurin (Alcaligenes faecalis, strain S-6) (1paz: 1paz [1aaj] [1plc]) {Greek anti beta + wedge alpha} [plasto] XXX Thornton Greek 2 #1paz 1.55 monomer [123]; oxidized Cu++ at pH 6.8; 93 HOHs #2paz 2.0 monomer [123]; 1 Cu++ and 89 HOHs Purine Nucleoside Phosphorylase (Homo sapiens) (1ula: 1ula) {domain 1: 1-109: a/b/c doubly wound mixed beta ud+cr/cr} {domain 2: 110-289: a/b/c doubloy wound mixed beta cr/cr + alpha} #1ula 2.75 trimer - 1 chain given [289]; supersedes 2pnp; 2 SO4s #1ulb 2.75 trimer - 1 chain given [289]; 1 guanine and 2 SO4s Alpha-1-Purothionin (Triticum aestivum) {SS rich a/b/c doubly folded anti beta} #2plh 2.5 monomer [45]; 10 DISs, 3 ACTs, 2 SBTs, 1 PO4, 2 GOLs, and 98 HOHs; 4 SSs Putidaredoxin (Pseudomonas putida, strain ATCC 17453) {domain 1: 1-40,88-107: a/b open face mixed beta cr} {domain 2: 41-87: encircled axial beta + alpha} XXX #1put NMR monomer [106]; 1 FES Inorganic Pyrophosphatase (Escherichia coli) {a/b/a doubly wound mixed beta cr/cr + anti beta + coil} #1eip 2.7 hexamer(a6) - 2 chains given [175] Inorganic Pyrophosphatase (Saccharomyces cerevisiae) (1pyp: 1pyp) {a/b/a doubly wound mixed beta cr/cr + anti beta + coil} [pyp] #1pyp 3.0 dimer (a2) - 1 chain given [285] Pyruvate Dehydrogenase Multienzyme Complex (Bacillus stearothermophilus) (1lac: 1lac) {double stranded anti beta cylinder} #1lab NMR monomer - 11 models given [80]; lipoylated domain of lipoamide acetyltransferase subunit #1lac NMR monomer - [80]; minimized average structure; lipoylated domain of lipoamide acetyltransferase subunit Pyruvate Kinase (Felis domestica) (1pyk: ???) {domain 1: 1-67,157-308: a/b singly wound para beta} [barrel+] {domain 2: 68-156: Greek anti beta} {domain 3: 309-432: a/b/a doubly wound para beta ud/cr + anti beta} #1pyk 2.6 CA tetramer (a4?) - 1 chain given [432]; all residues UNK Pyruvate Oxidase (Lactobacillus plantarum) (1pow.A: 1pow.A) {domain 1: 9-191: a/b/a doubly wound para beta ud/ud + anti beta} {domain 2: 192-343: a/b/a doubly wound para beta ud/cr} {domain 3: 344-365,548-593: wedge alpha} XXX c/a open face anti beta cr {domain 4: 366-547: a/b/a doubly wound para beta ud/ud} #1pow 2.5 tetramer (a4) - 2 chains given [585]; 2 Mg++s, 2 thiamin diphos- phates, 2 FADs, and 120 HOHs #1pox 2.1 tetramer (a4) - 2 chains given [585]; P178S, S188N, and A458V mutant; 2 Mg++s, 2 thiamin diphosphates, 2 FADs, 2 glycerols, 2 Na+s, and 739 HOHs Pyruvoyl-Dependent Histidine Decarboxylase (Lactobacillus sp., strain 30A) (1pya.A: 1pya.A) (1pya.B: 1pya.B) {back to back a/b open face anti beta cr/cr + anti beta + wedge alpha} #1pya 2.5 dodecamer (6ab) - 6 chains given [81, 228]; chains result from autocatalytic cleavage; 3 pyruvoyl groups and 471 HOHs c-H-RAS p21 Protein (Homo sapiens) (5p21: 5p21) {a/b/a doubly wound para beta ud/ud + a/b/a doubly wound mixed beta ud/ud} XXX Thornton dw1 #121p 1.54 monomer? [166]; catalytic domain; 1 GTP with O3B replaced by C3B, 1 Mg++, and 195 HOHs #221p 2.3 monomer? [166]; catalytic domain; D38E mutant; 1 GTP with O3B replaced by N3B, 1 Mg++, and 210 HOHs #421p 2.2 monomer? [166]; catalytic domain; G12R mutant; 1 GTP with O3B replaced by N3B, 1 Mg++, and 202 HOHs #521p 2.6 monomer? [166]; catalytic domain; G12V, A59T mutant; 1 GTP and Mg #621p 2.4 monomer? [166]; catalytic domain; Q61H mutant; 1 GTP with O3B replaced by N3B, 1 Mg++, and 226 HOHs #721p 2.0 monomer? [166]; catalytic domain; Q61L mutant; 1 GTP with O3B replaced by N3B, 1 Mg++, and 191 HOHs #821p 1.5 monomer? [166]; catalytic domain; G12P; 1 GTP with O3B replaced by with O3B replaced by N3B, 1 Mg++, and 118 HOHs #1agp 2.3 monomer? [166]; catalytic domain; G12D mutant; 1 guanosine-5'- (beta,gamma-imido) triphosphate, 1 Mg++, and 39 HOHs #1crp NMR monomer - 20 models given [166]; catalytic domain; 1 GDP, 1 Mg++, and 4 HOHs #1crq NMR monomer [166]; catalytic domain; minimized average structure; 1 GDP, 1 Mg++, and 4 HOHs #1crr NMR monomer - 20 models given [166]; catalytic domain; "final 20 structures"; 1 GDP, 1 Mg++, and 4 HOHs #5p21 1.35 monomer? [166]; catalytic domain; 1 guanosine-5'-(beta,gamma- imido) triphosphate, 1 Mg++ and 211 HOHs #1q21 2.2 monomer? [171]; supersedes 2p21; catalytic domain; 1 Mg++ (or Ca++), 1 GDP, and 39 HOHs #2q21 2.2 monomer? [171]; supersedes 3p21; catalytic domain; G12V mutant; 1 Mg++ (or Ca++), 1 GDP, and 40 HOHs #4q21 2.2 monomer? [189]; catalytic domain; 1 Mg++ (or Ca++), 1 GDP, and 78 HOHs #6q21 1.95 monomer? - 4 chains given [171]; catalytic domain; chain C is best ordered; 4 Mg++s (or Ca++s), 4 GDPCPs, and 453 HOHs Rat Mast Cell Protease II (Rattus rattus) (3rp2.A: 3rp2.A [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [1ton] [1sgt] [1hne.E]) {domain 1: Greek anti beta} {domain 2: Greek anti beta} [s_prot+] #3rp2 1.9 monomer - 2 chains given [224]; 123 HOHs; 6 SSs Rec-A Protein (Escherichia coli) (2reb: 2reb) {domain 1: 3-23: alpha} {domain 2: 24-55,221-269: a/b open face anti beta ud} {domain 3: 56-220: a/b/a doubly wound para beta ud/ud} {domain 4: 270-328: a/a partially encircled axial alpha + anti beta} #1rea 2.7 CA monomer? [352]; 1 ADP #2reb 2.3 monomer? [352]; 136 HOHs Recoverin (Bos taurus) (1rec: 1rec [2sas] [4icb] [1osa] [1rro] [4cpv]) {domain 1: 9-97: Greek anti alpha} {domain 2: 98-198: } [ca_bind+] XXX check for domains; homology to calmodulin #1rec 1.9 monomer? [201]; 1 Ca++ and 164 HOHs Relaxin (Sus scrofa) (1rlx.A: 6rlx.A) (1rlx.B: 6rlx.B) {SS rich a/a open face anti alpha + anti beta} #1rlx --- tetramer - 2 chains given [22, 30]; non-experimental; based on insulin; 3 SSs #2rlx --- tetramer - 2 chains given [22, 30]; non-experimental; 3 SSs #3rlx --- tetramer - 2 chains given [22, 30]; non-experimental; 3 SSs #4rlx --- tetramer - 2 chains given [22, 30]; non-experimental; 3 SSs Relaxin (Homo sapiens) (6rlx.A: 6rlx.A) (6rlx.B: 6rlx.B) {SS rich a/a open face anti alpha + anti beta} #6rlx 1.5 tetramer (a2b2) - 4 chains given [24, 28]; 73 HOHs; 6 SSs Renin (Homo sapiens) (1rne: 1smr.A [3psg] [1lya.B] [1mpp] [2apr]) {domain 1: multiple anti beta + alpha} [ac_prot+] XXX {domain 2: multiple anti beta + alpha} [ac_prot+] #1bbs 2.8 monomer? [335]; recombinant glycosylated form; 3 SSs #1rne 2.4 monomer? [340]; 1 NAG, 1 transition state analogue CGP38'560, and 138 HOHs; 3 SSs #2ren 2.5 monomer? [340]; 1 NAG; 3 SSs Renin (Mus musculus) (1smr.A: 1smr.A [3psg] [1lya.B] [1mpp] [2apr]) {domain 1: multiple anti beta + alpha} [ac_prot+] XXX {domain 2: multiple anti beta + alpha} [ac_prot+] #1smr 2.0 monomer + inhibitor - 2 chains given [335, 9]; inhibitor CH-66; 1 pivalic acid, 1 Leu-hydroxyethylene-Leu and 156 HOHs; 3 SSs Repressor of Primer (ColE1 ROP) (Escherichia coli) (1rop.A: 1rop.A) {up down anti alpha pair} #1rop 1.7 dimer (a2) - 1 chain given [63]; 48 HOHs #1rpr NMR dimer (a2) - 10 models of 2 chains given [63] Epididymal Retinoic Acid Binding Protein (Rattus norvegicus) {up down anti beta + alphas} #1epa 2.1 dimer (a2) - 2 chains given [164]; 119 HOHs; B-Form #1epb 2.2 dimer (a2) - 2 chains given [164]; 2 REAs and 72 HOHs; B-Form Retinoic Acid Receptor (Homo sapiens) (1hra: 1hra [1glu.A]) {metal binding crossed alpha + anti beta + coil} #1hra NMR fragment - 15 models given [80]; beta DNA-binding domain; 2 Zn++s Retinol Binding Protein (Bos taurus) (1hbq: 1hbq [1bbp.A] [2apd]) {up down anti beta + coil caps + ud alpha} #1erb 1.9 monomer? [183]; 1 N-ethyl retinamide and 160 HOHs; 3 SSs #1fel 1.8 monomer? [183]; 1 FEN and 163 HOHs; 3 SSs #1fem 1.9 monomer? [183]; 1 REA and 164 HOHs; 3 SSs #1fen 1.9 monomer? [183]; 1 AZE and 162 HOHs; 3 SSs #1hbp 1.9 monomer? [183]; holo; 1 retinol and 164 HOHs; 3 SSs #1hbq 1.7 monomer? [183]; apo; 166 HOHs; 3 SSs Retinol Binding Protein (Homo sapiens) (1rbp: 1hbq [1bbp.A] [2apd]) {up down anti beta + coil caps + ud alpha} XXX Thornton orthogonal barrel #1brp 2.5 monomer [182]; holo; 1 retinol and 54 HOHs; 3 SSs #1brq 2.5 monomer [182]; apo; 55 HOHs; 3 SSs #1rbp 2.0 monomer [182]; 1 retinol and 153 HOHs; 3 SSs Cellular Retinol Binding Protein II (Escherichia coli) (1opb.A: 1opb.A [1icm] [2hmb] [1mdc]) {up down anti beta + anti alpha cap} #1opa 1.9 monomer? - 2 chains given [135]; apo form; 89 HOHs #1opb 1.9 monomer? - 4 chains given [135]; holo form; 4 retinals and 157 HOHs Rhinovirus 14 Coat Protein (Homo sapiens) (4rhv.1: 4rhv.1 [2plv.1] [1r1a.1]) {Greek anti beta} [virus] XXX (4rhv.2: 2plv.2 [1bbt.2] [1tme.2]) {Greek anti beta} [virus] (4rhv.3: 4rhv.3 [1bbt.3] [2plv.3] [1tme.3]) {Greek anti beta} [virus] (4rhv.4: 4rhv.4 [1r1a.4]) {coil + alpha} #240mer (60abcd) - 4 chains given [289, 262, 236, 68]; icosohedral #1hri 3.0 240mer - 4 chains given [289, 262, 236, 68]; 2:I170L strain; (1-[6-(2-chloro-4-methoxyphenoxy)-hexyl]imidazole hydrochloride #1r08 3.0 with antiviral agent (WIN VIII) #1r09 2.9 with antiviral agent (WIN R61837); dimethyl sulfoxide; 198 HOHs #2r04 3.0 supersedes 1r04; with antiviral agent (WIN IV); 4 HOHs #2r06 3.0 supersedes 1r06; with antiviral agent (WIN VI); 5 HOHs #2r07 3.0 supersedes 1r07; with antiviral agent (WIN VII) #4rhv 3.0 supersedes 2rhv; 274 HOHs #2rm2 3.0 supersedes 1rm2; with antiviral agent (WIN II); 2 HOHs #1rmu 3.0 1:C199Y mutant; 1 Tris+ and 261 HOHs #2rmu 3.0 1:V188L mutant; 272 HOHs #2rr1 3.0 supersedes 1rr1; with antiviral agent (WIN I[R]); 7 HOHs #2rs1 3.0 supersedes 1rs1; with antiviral agent (WIN I[S]); 8 HOHs #2rs3 3.0 supersedes 1rs3; with antiviral agent (WIN III[S]); 4 HOHs #2rs5 3.0 supersedes 1rs5; with antiviral agent (WIN V[S]); 2 HOHs Rhinovirus Serotype 1A Coat Protein (Homo sapiens) (1r1a.1: 1r1a.1 [2plv.1] [4rhv.1]) {Greek anti beta} [virus] XXX (1r1a.2: 2plv.2 [1bbt.2] [1tme.2]) {Greek anti beta} [virus] (1r1a.3: 4rhv.3 [1bbt.3] [1tme.3] [2plv.3]) {Greek anti beta} [virus] (1r1a.4: 2plv.4) {coil} #1r1a 3.2 240mer (60abcd) - 4 chains given [287, 263, 238, 44]; icoso- hedral; 1 sucrose and 274 HOHs Rhodanese (Bos taurus) (1rhd: 1rhd) {domain 1: 1-151: a/b/a doubly wound para beta cr/cr} [rhd] {domain 2: 152-293: a/b/a doubly wound para beta ud/cr} [rhd] #1rhd 2.5 monomer [293]; S bonded to SG of C247 Ribonuclease A (Bos taurus) (7rsa: 7rsa) {SS rich a/b open face anti beta cr + a/b open face anti beta cr + alpha} [rna] #2aas NMR monomer - 32 models given [124]; 4 SSs #1rar 1.9 monomer [123]; 1 acetylaminoethyl naphthylamine sulfonate, 3 Cl-s, and 104 HOHs; 4 SSs #1ras 1.7 monomer [123]; ammonium sulfate crystal type; 1 acetylaminoethyl naphthylamine sulfonate and 100 HOHs; 4 SSs #1rat 1.5 monomer [124]; temp: 98K #2rat 1.5 monomer [124]; temp: 130K #3rat 1.5 monomer [124]; temp: 160K #4rat 1.5 monomer [124]; temp: 180K #5rat 1.5 monomer [124]; temp: 220K #6rat 1.5 monomer [124]; temp: 240K #7rat 1.5 monomer [124]; temp: 260K #8rat 1.5 monomer [124]; temp: 300K #9rat 1.5 monomer [124]; temp: 320K #1rbb 2.5 monomer - 2 chains given [124]; B #1rbc 2.0 monomer (cleaved, ab) - 2 chains given [16, 104]; M13A mutant; 1 SO4, 1 terminal amide, and 56 HOHs; 4 SSs #1rbd 1.7 monomer (cleaved, ab) - 2 chains given [16, 104]; M13ABA mutant; 1 ABA, 1 terminal amide, 1 SO4, and 57 HOHs; 4 SSs #1rbe 1.75 monomer (cleaved, ab) - 2 chains given [16, 104]; M13F mutant; 1 terminal amide, 1 SO4, and 63 HOHs; 4 SSs #1rbf 1.8 monomer (cleaved, ab) - 2 chains given [16, 104]; M13G mutant; 1 terminal amide, 1 SO4, and 62 HOHs; 4 SSs #1rbg 1.8 monomer (cleaved, ab) - 2 chains given [16, 104]; M13I mutant; 1 terminal amide, 1 SO4, and 57 HOHs; 4 SSs #1rbh 1.7 monomer (cleaved, ab) - 2 chains given [16, 104]; M13L mutant; 1 terminal amide, 1 SO4, and 58 HOHs; 4 SSs #1rbi 1.8 monomer (cleaved, ab) - 2 chains given [16, 104]; M13V mutant; 1 terminal amide, 1 SO4, and 60 HOHs; 4 SSs #3rn3 1.45 monomer [124]; supersedes 1rn3; 1 SO4 anion and 107 HOHs; 4 SSs #1rnc 1.5 monomer [124]; 1 cytidylyl-2'5'-phosphoryl guanosine, 1 SO4, and 30 HOHs; 4 SSs #1rnd 1.5 monomer [124]; 1 deoxycytidylyl-3',5'-guanosine, 1 SO4, and 96 HOHs; 4 SSs #2rns 1.6 monomer (cleaved, ab) - 2 chains given [20, 104]; S; supersedes 1rns; pH 4.75; 1 SO4 and 83 HOHs; 4 SSs #1rnu 1.6 monomer [124]; S; pH 5.5; 1 SO4 and 88 HOHs; 4 SSs #1rnv 1.6 monomer [124]; S; pH 4.75; 1 SO4 and 70 HOHs; 4 SSs #1rob 1.6 monomer [124]; 1 cytidine 2'-monophosphate and 101 HOHs; 4 SSs #5rsa 2.0 monomer [124]; joint x-ray & neutron; supersedes 4rsa; 1 phos- phate and 128 deuterated HOHs; 4 SSs #6rsa 2.0 monomer [124]; joint x-ray & neutron; 1 uridine vanadate and 128 deuterated HOHs; 4 SSs #7rsa 1.26 monomer [124]; phosphate-free; joint x-ray & neutron; 1 2-methyl- 2-propanol and 189 deuterated HOHs; 4 SSs #8rsa 1.8 monomer (a2) - 2 chains given [124]; phosphate-free; 2 N-acetyl- deoxythymidines and 246 HOHs; 8 SSs #9rsa 1.8 dimer (a2) - 2 chains given [124]; phosphate-free; 2 N-acetyl- deoxyuridines and 181 HOHs; 8 SSs #1rsm 2.0 monomer [124]; 1 dinitrophenylene crosslinking 7 and 41; 75 HOHs; 4 SSs #1rta 2.5 monomer + nucleotide - 2 chains given [124, 4]; nucleotide is TTTT; 4 SSs #1rtb 2.5 monomer [124]; 4 SSs #1srn 1.8 monomer (cleaved, ab) - 2 chains given [118, 14]; semi-synthetic; 1 SO4 and 115 HOHs; 4 SSs Ribonuclease BS (Bos taurus) (1bsr.A: 7rsa) {a/b open face anti beta cr + a/b open face anti beta cr + alpha} #1bsr 1.9 dimer (a2) - two chains given [124]; 7 SO4s and 113 HOHs; 10 SSs Ribonuclease F1 (Fusarium moniliforme) (1fus: 9rnt) {a/b open face anti beta cr + anti beta} XXX Thornton twisted beta #1fus 1.3 monomer [106]; 107 HOHs; 2 SSs #1fut 2.0 monomer [106]; 1 2GP and 46 HOHs; 2 SSs Ribonuclease H (Escherichia coli) (2rn2: 2rn2) {a/b/a doubly wound anti beta ud/ud + para beta + wedge alpha} #1goa 1.9 monomer [156]; Ins(80G81) mutant; 92 HOHs #1gob 2.0 monomer [155]; G77A mutant; 114 HOHs #1goc 2.0 monomer [155]; G77A and Ins(80G81) mutant; 87 HOHs #1lav 1.8 monomer [155]; V74L mutant; 117 HOHs #1law 1.8 monomer [155]; V74I mutant; 111 HOHs #1rbr 1.8 monomer [155]; H62P mutant; 116 HOHs #1rbs 1.8 monomer [155]; H62A mutant; 110 HOHs #1rbt 1.8 monomer [155]; K95G mutant; 121 HOHs #1rbu 1.8 monomer [155]; K95N mutant; 111 HOHs #1rbv 1.8 monomer [155]; K95A mutant; 104 HOHs #1rda 2.15 monomer [155]; D10N mutant; 100 HOHs #1rdb 1.9 monomer [155]; E48Q mutant; 97 HOHs #1rdc 2.3 monomer [155]; D70N mutant; 121 HOHs #1rdd 2.8 monomer [155]; HI; 1 Mg++ and 35 HOHs #1rnh 2.0 monomer [155]; 4 selenomethionines in place of methionines, 1 SO4, and 86 HOHs #2rn2 1.48 monomer [155]; 225 HOHs Ribonuclease H (Thermus thermophilus, HB8) (1ril: 2rn2) {a/b/a doubly wound anti beta ud/ud + para beta + wedge alpha} #1ril 2.8 monomer [166] Ribonuclease Ms (Aspergillus saitoi) (1rds: 9rnt) {a/b open face anti beta cr + anti beta} #1rds 1.8 monomer [105]; 1 2'-fluoroguanylyl-(3'-5')-cytidine and 31 HOHs; 2 SSs #1rms 1.9 monomer [105]; 1 3'-guanylic acid and 24 HOHs; 2 SSs Ribonuclease Sa (Streptomyces aureofaciens) (1sar.A: 1sar.A) {a/b open face anti beta cr} XXX Thornton twisted beta #1gmp 1.7 monomer - 2 chains given [96]; 2 2GPs, 1 SO4, and 492 HOHs; EMBL data used; 2 SSs #1gmq 1.8 monomer - 2 chains given [96]; 1 SO4 and 423 HOHs; data from synchrotron and Hamburg imaging plate; 2 SSs #1gmr 1.77 monomer - 2 chains given [96]; 2 2GPs, 1 SO4, and 388 HOHs; UCLA data used; 2 SSs #1sar 1.8 monomer - 2 chains given [96]; 1 SO4 and 240 HOHs; 2 SSs #2sar 1.8 monomer - 2 chains given [96]; 1 3'-guanylic acid (GMP), 2 sul- fates, and 222 HOHs; 2 SSs Ribonuclease T1 (Aspergillus oryzae) (9rnt: 9rnt) {a/b open face anti beta cr + anti beta} [rnt] XXX Thornton twisted beta #2aad 2.0 monomer - 2 chains given [104]; isozyme 2' - H40K mutant; 2 2GPs, 2 Ca++s, and 239 HOHs; 4 SSs #2aae 1.8 monomer [104]; isozyme 2' - H40K mutant; 1 Ca++, 1 phosphate, and 116 HOHs; 2 SSs #1lra 1.9 monomer [104]; E58A mutant; 1 2GP, 1 Na+ and 90 HOHs; 2 SSs #1rga 1.7 monomer [104]; Q25K variant; 1 GMP, 1 Ca++, and 142 HOHs; 2 SSs #1rgc 2.0 monomer - 2 chains given [104]; Q25K variant; 2 GMPs, 2 Ca++s, and 180 HOHs; 4 SSs #1rgk 1.87 monomer [104]; E46Q mutant; 2'AMP, 1 Ca++, and 86 HOHs; 2 SSs #1rgl 2.0 monomer [104]; E46Q mutant; 2GP, 1 Ca++, and 81 HOHs; 2 SSs #1rn1 1.84 monomer - 3 chains given [104]; K25Q, 25Q variant; 3 SO4s and 179 HOHs; 6 SSs #1rn4 1.8 monomer [104]; H92A mutant; 1 Ca++ and 82 HOHs; 2 SSs #1rnt 1.9 monomer [104]; 1 2GP and 91 HOHs; 2 SSs #2rnt 1.8 monomer [104]; 1 guanylyl-2'5'-guanosine, 1 Ca++, and 105 HOHs; 2 SSs #3rnt 1.8 monomer [104]; 1 Ca++, 1 vanadate, and 162 HOHs; 2 SSs #4rnt 2.2 monomer [104]; H92A mutant; 70 HOHs; 2 SSs #5rnt 3.2 monomer [104]; 1 guanosine-3'5'-bisphosphate; 83 HOHs; 2 SSs #6rnt 1.8 monomer [104]; 1 2'-adenylic acid, 1 Ca++, and 104 HOHs; 2 SSs #7rnt 1.9 monomer [104]; Y45W mutant; 1 2'-adenylic acid, 1 Ca++, and 75 HOHs; 2 SSs #8rnt 1.8 monomer [104]; 1 Zn++ and 104 HOHs; 2 SSs #9rnt 1.5 monomer [104]; 1 Ca++ and 121 HOHs; 2 SSs Ribonuclease Inhibitor (Sus scrofa) {a/b singly wound para beta} *good for structure picture: super TIM barrel #1bnh 2.3 monomer? [456] Protein R2 of Ribonucleotide Reductase (Escherichia coli) (1rib.A: 1rib.A) {up down anti alpha 6 helix bundle + crossed anti alpha pair + anti beta + alphas} #1mrr 2.5 dimer? (a2) - 2 chains given [375]; 4 Mn++s, 13 Hg++s, and 233 HOHs; 1 SS #1rib 2.2 dimer? (a2) - 2 chains given [375]; 2 mu-oxo-diirons and 325 HOHs #1rnr 2.5 dimer? (a2) - 2 chains given [375]; F208Y mutant, converted to dihydroxy phenylalanine; 4 HYDs, 4 Fe+++s, 14 Hg++s, and 137 HOHs D-Ribose Binding Protein (Escherichia coli, K12) (2dri: 2dri [1gca]) {domain 1: 1-104,237-263: a/b/a doubly wound para beta ud/ud} {domain 2: 105-236,264-271: a/b/a doubly wound para beta ud/ud + anti beta strand} [binding+] #1dbp 1.7 monomer [271]; G72D mutant; 1 RIP and 166 HOHs #2dri 1.7 monomer [271]; supersedes 1dri; 1 RIP and 216 HOHs Ribosomal Protein S5 (Bacillus stearothermophilus) (1pkp: 1pkp) {domain 1: 4-75: a/b open face anti beta cr} {domain 2: 76-148: a/b open face anti beta cr} #1pkp 2.8 monomer [150] Ribosomal Protein S17 (Bacillus stearothermophilus) (1rip: 1rip) {open face anti beta + anti beta} #1rip NMR monomer? - 6 models given [81] 5S Ribosomal RNA (Escherichia coli) #1elh NMR fragments - 2 chains given [12, 13] 5S Ribosomal RNA (Xenopus laevis) #1rrn --- monomer [118]; non-experimental model Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) (Nicotiana tabacum) (3rub.L: 3rub.L [5rub.A]) (3rub.S: 3rub.S) {domain 1: L22-147: a/b open face anti beta cr} {domain 2: L148-492: a/b singly wound para beta + wedge alpha} {domain 3: S1-123: a/b open face anti beta ud} #1rlc 2.7 dimer (ab) - 2 chains given [477, 123]; 1 2-carboxy-D-arabinitol 1,5-bisphosphate (transition state analogue); 1 SS #3rub 2.0 dimer (ab) - 2 chains given [477, 123]; form III; 3 SO4s and 216 HOHs; 1 SS #4rub 2.7 dimer (ab) - 8 chains given [477, 123]; form IV; A:M405G, S:E88G variant; 4 carboxylic groups on A:K201s, 4 2-carboxyarabinitol- 1,5-biphosphates, and 4 Mg++s; 10 SS Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) (Rhodospirillum rubrum) (5rub.A: 5rub.A [3rub.L]) {domain 1: 2-135: a/b/c doubly wound anti beta cr/cr} {domain 2: 136-420: a/b singly wound para beta} {domain 3: 421-457: single stranded alpha cylinder} #1rba 2.6 dimer (a2) - 2 chains given [466]; D193N mutant; 110 HOHs #5rub 1.7 dimer (a2) - 2 chains given [490]; fusion protein with 24 residues of beta galactosidase at N-terminus; supersedes 2rub; 736 HOHs #9rub 2.6 dimer (a2) - 2 chains given [466]; 2 carboxylic groups on K191s, 2 ribulose-1,5-bisphosphates, and 2 Mg++s #1rus 2.9 dimer (a2) - 2 chains given [490]; fusion protein as 5rub; 2 3-phosphoglycerates #2rus 2.3 dimer (a2) - 2 chains given [490]; fusion protein as 5rub; 2 carbamyl activator groups, 2 Mg++s, and 714 HOHs Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) (Spinacia oleracia) (8rub.L: 3rub.L [5rub.A]) (8rub.S: 3rub.S) {domain 1: L9-147: a/b open face anti beta cr} {domain 2: L148-476: a/b singly wound para beta + wedge alpha} {domain 3: S: a/b open face anti beta ud} #8rub 2.4 16mer? (a8b8) - 2 chains given [123, 475]; 1 Mg++, 1 carboxylic group (on Lys 201), and 1 2-carboxyarabinitol-1,5-bisphosphate RNA (Synthetic) #1rna 2.25 dimer (a2) - 2 chains given; UUAUAUAUAUAUAA; 91 HOHs RNA 5'-UGGGGU-3' (Synthetic) #1rau NMR tetramer (a4) - 1 model of 4 chains given RNA, Group I Introns of Large Ribosomal Precursor RNA (Tetrahymena thermophila) #1ipt --- oligomer - 7 chains given [5, 13, 22, 18, 31, 19, 10]; non-ex- perimental model; core structure Ricin (Ricinus communis) (2aai.A: 2aai.A) (2aai.B: 2aai.B) {domain 1: A1-181: a/b/c doubly wound anti beta cr/ud + alphas} {domain 2: A182-267: a/b open face anti beta + crossed alpha} {domain 1: B1-139: 6 anti beta pairs on cube faces} {domain 2: B140-262: 6 anti beta pairs on cube faces} #2aai 2.5 dimer (ab) - 2 chains given [267, 262]; 2 GALs, 2 GLCs, 6 MANs, 4 NAGs, and 123 HOHs; 5 SSs #1apg 3.0 monomer + dinucleotide - 2 chains given [267, 2]; chain A only; 1 adenyl-3'-5' guanosine #1fmp 2.8 dimer (ab) - 1 chain given [267]; chain A only; 1 formycin mono- phosphate #1rtc 2.3 dimer (ab) - 1 chain given [268]; chain A only; 48 HOHs Rous Sarcoma Virus Protease (Rous Sarcoma virus, strain PR-C) (2rsp.A: 2rsp.A) {Greek anti beta + anti beta + coil} [virus_prot] XXX Thornton twisted sheet #2rsp 2.0 dimer (a2) - 2 chains given [124]; 252 HOHs; res 82 L vs. V in 1mvp, otherwise identical RP 71955 (Actinomycetes, strain sp9440) (1rpb: 1rpb) {SS rich open face anti beta} #1rpb NMR monomer [21]; tricyclic peptide active against HIV-1; minimized mean structure; 2 SSs #1rpc NMR monomer - 20 models given [21]; tricyclic peptide active against HIV-1; SA structures; 2 SSs each Rubredoxin (Clostridium pasteurianum) (5rxn: 8rxn.A [6rxn]) {metal binding crossed anti beta+coil + anti beta} [rdx] #4rxn 1.2 monomer [54]; oxidized; unconstrained; supersedes 2rxn; 1 Fe+++ and 127 HOHs #5rxn 1.2 monomer [54]; oxidized; constrained; supersedes 2rxn; 1 Fe+++ and 102 HOHs Rubredoxin (Desulfovibrio desulfuricans, strain 27774) (6rxn: 6rxn [8rxn.A]) {metal binding crossed anti beta+coil + anti beta} [rdx] #6rxn 1.5 monomer [46]; 1 Fe and 121 HOHs Rubredoxin (Desulfovibrio gigas) (1rdg: 8rxn.A [6rxn]) {metal binding crossed anti beta + anti beta} [rdx] #1rdg 1.4 monomer [53]; oxidized; 1 Fe+++ and 117 HOHs Rubredoxin (Desulfovibrio vulgaris) (7rxn: 8rxn.A [6rxn]) {metal binding crossed anti beta + anti beta} [rdx] #7rxn 1.5 monomer [52]; supersedes 3rxn; 1 Fe+++, 1 SO4, and 180 HOHs #8rxn 1.0 monomer [52]; 1 Fe++, 1 SO4, and 102 HOHs Rubredoxin (Pyrococcus furiosus) (1caa: 8rxn.A [6rxn]) {metal binding crossed anti beta+coil + anti beta} [rdx+] #1caa 1.8 monomer [53]; oxidized; 1 Fe+++ and 61 HOHs #1cad 1.8 monomer [53]; reduced; 1 Fe+++ and 36 HOHs #1zrp NMR monomer - 40 models given [53]; 1 Zn++ Sarcoplasmic Calcium-Binding Protein (Brancheostoma lanceolatum) (2sas: 2sas [4icb] [1osa] [1rro] [4cpv] [1rec]) {crossed alpha + anti beta} #2sas 2.4 monomer? [185]; isotype II; 3 Ca++s and 1 HOH; 1 SS; compact form Sarcoplasmic Calcium-Binding Protein (Nereis diversicolor) (2scp.A: 2scp.A) {crossed alpha + anti beta} XXX Thornton EF hand #2scp 2.0 monomer - 2 chains given [174]; 6 Ca++s and 213 HOHs Satellite Tobacco Necrosis Virus (STNV) (2stv: 2stv) {double stranded beta cylinder + alpha} [virus] XXX Thornton Jelly Roll #2stv 2.5 60mer (a60) - 1 chain given [195]; 3 Ca++s and 158 HOHs Scorpion Neurotoxin Variant 3 (Centruroides sculpturatus Ewing) (2sn3: 2sn3) {SS rich a/b open face anti beta cr} [sn3] #2sn3 1.2 monomer [65]; supersedes 1sn3; 1 2-methyl-2,4-pentanediol and 125 HOHs; 4 SSs Scorpion Toxin (Androctonus mauretanicus mauretanicus) (1pnh: 1pnh) {SS rich a/b open face anti beta ud} zinc finger-like? #1pnh NMR monomer - 25 models given [31]; 3 SSs Sendai Virus Nucleoprotein (SEV-9) (1vab.P: 1vab.P) {coil} DUP1vab 2.5 fragment + microglobulin + MHC - 3 chains given [9, 99, 274]; 91 HOHs; 3 SSs Serine Carboxypeptidase II (Triticum vulgaris) (3sc2.A: 3sc2.A) (3sc2.B: 3sc2.B) XXX check on cleavage and domains {domain 1: A:-4-180,B:264-422: a/b/a doubly wound para beta ud/ud + a/b/c doubly wound anti beta ud/cr + andti beta + crossed alpha} {domain 2: A:181-247: up down anti alpha 3 helix bundle} #3sc2 2.2 dimer (ab) - 2 chains given [259, 152]; supersedes 2sc2; 6 NAGs, 2 MANs, 2 FUCs, and 197 HOHs; 3 SSs Serratia Metallo Proteinase (Serratis marcenscens) { #1smp Seryl-tRNA Synthetase (Thermus thermophilus, strain HB27) (1sry.A: 1sry.A) {domain 1: 1-101: up down anti alpha pair} {domain 2: 102-421: a/b/a doubly wound anti beta ud/cr + a/b open face anti beta ud + crossed alpha + alpha} #1sry 2.5 dimer? (a2) - 2 chains given [421]; 190 HOHs Sialidase (Salmonella typhimurium LT2) (1sim: 1sim) {6 X 3-4 anti beta wheel + alphas} #1sil 2.2 monomer? [381]; 1 2-deoxy-2,3,-dehydro-N-acetyl-neuraminic acid, and 140 HOHs; 1 SS #1sim 2.0 monomer? [381]; 95 HOHs; 1 SS Silk Fibroin (Bombyx mori) (1slk.A: 1slk.A) {multi-strand anti beta} (1slk.F: 1slk.F) {multi-strand anti beta} #1slk --- multimer - 15 chains given [8]; non-experimental; form I; 8 N- methylamide #2slk --- multimer - 15 chains given [8]; non-experimental; form II; 15 N- methyl amines Simian Immunodeficiency Virus Protease (Simian Immunodeficiency Virus, MAC251) (1siv.A: 2mip.A [5hvp.A]) {Greek anti beta + anti beta + alpha} [virus_prot+] 3 layer 3 loop #1siv 2.5 dimer? (a2) - 2 chains given [99]; 1 ala-ala-phe-psh((S)-CHOH- CH2)-gly-val-val-ome and 34 HOHs Sindbis Virus Capsid Protein (Sindbis virus) (2snv: 2snv) {domain 1: 114-177: c/b open face anti beta + anti beta} {domain 2: 178-264: Greek anti beta + anti beta loop} XXX Thornton Greek #2snv 2.8 dimer (a2) - 1 chain given [151]; core protein #1snw 3.0 dimer (a2) - 2 chains given [151]; core protein Somatotropin (Bos taurus) (1bst: 1huw) {up down anti alpha 4 helix bundle + alpha} #1bst --- monomer? [191]; non-experimental model; 2 SSs Sorbitol Dehydrogenase (Ovis aries) (1sdg: 1sdg [2ohx.A]) {domain 1: 4-169: c/b open face anti beta + anti beta + alpha} {domain 2: 170-344: a/b/a doubly wound para beta ud/ud + alpha} {domain 3: 345-374: a/b open face para beta ud} [nbd+] #1sdg --- monomer? [347]; 1 NAD, 1 Zn, and 1 SOR; non-experimental Southern Bean Mosaic Virus Coat Protein (SBMV) (4sbv.A: 4sbv.A) {double stranded beta cylinder + alphas} [virus] XXX Thornton Jelly Roll #4sbv 2.8 540mer (a540) - 3 chains given [261]; supersedes 3sbv; 3 Ca++s and 34 HOHs; 3 SSs Alpha Spectrin (Gallus gallus) (1shg: 1shg [1shf.A] [1hsp]) {Greek anti beta} #1shg 1.8 monomer [62]; SH3 domain Staphylococcyl Nuclease (Staphylococcus aureus) (2sns: 2sns) {Greek anti beta + cap alpha + c/a open face para alpha + alpha} XXX [sns] #1ena 2.15 monomer [135]; D21E mutant; FOGGI strain; 1 Ca++ and 34 HOHs #1enc 1.95 monomer [135]; D21E mutant; FOGGI strain; 1 PTP, 1 Ca++ and 41 HOHs #1kaa 1.9 monomer [136]; K116A mutant; FOGGI strain; 63 HOHs #1kab 1.8 monomer [136]; K116G mutant; FOGGI strain; 60 HOHs #1snc 1.65 monomer [149]; 1 3',5'-deoxythymidine bisphosphate; 1 Ca++ and 82 HOHs; 3 residues differ from 2sns #1snm 1.74 monomer [149]; E43D mutant; 1 3',5'-deoxythymidine bisphosphate, 1 Ca++, and 60 HOHs #2snm 1.97 monomer [149]; V66K mutant; 1 2'-deoxythymidine 3',5'-diphos- phate, 1 Ca, and 41 HOHs #2sns 1.5 monomer [149]; supersedes 1sns; 1 2'deoxy-3'5'-diphosphothymi- dine; 1 Ca++ #1sty 1.67 monomer [150]; Ins(126G127) mutant; 1 deoxythymidine-3'5'-bis- phosphate, 1 Ca++, and 147 HOHs Streptavidin (Streptomyces avinidii) (1pts.A: 1pts.A) {up down anti beta} #1pts 2.0 monomer? + peptide (2a + p) - 3 chains given [121, 7]; 241 HOHs #1stp 2.6 fragment [159]; 1 biotin and 84 HOHs Streptomyces Subtilisin Inhibitor (Streptomyces albogriseolus, S-3253 and Streptomyces lividans) (2ssi: 2ssi) {SS rich a/b open face anti beta cr} [ssi] DUP2sic 1.8 dimer + protease (i2 + a + a) - 2 chains given [107, 275]; super- sedes 1sic; inhibitor is a dimer & binds 2 subtilisins; 2 Ca++s and 258 HOHs; 2 SSs DUP3sic 1.8 inhibitor + subtilisin BPN' (a + a + i2) - 2 chains given [107, 275]; M73K mutant; lividans; inhibitor is a dimer & binds 2 sub- tilisins; 2 Ca++s and 273 HOHs; 2 SSs DUP5sic 2.2 monomer? + protease (i + a) - 2 chains given [107, 275]; M70G, M73K mutant; 2 Ca++s and 288 HOHs; 2 SSs #2ssi 2.6 dimer (a2) - 1 chain given [113]; supersedes 1ssi; 2 SSs DUP2tld 2.6 dimer + protease (i2 + a + a) - 2 chains given [110, 223]; inhibitor is a dimer & binds 2 trypsins; M70G and M73K mutant; 8 SSs Subtilisin BL (Bacillus lentus) (1st3: 1cse.E [1thm] [2pkc]) {a/b/a doubly wound para beta ud/ud + c/b open face para beta ud + anti betas + crossed alphas} #1st3 1.4 monomer? [269]; 2 Ca++s and 157 HOHs Subtilisin BPN (Novo) (Bacillus amyloliquefaciens) (1sbt: 1cse.E [1thm] [2pkc]) {a/b/a doubly wound para beta ud/ud + c/b open face para beta ud + alpha} [sbt] #1sbt 2.5 monomer [275]; BPN; 17 HOHs #2sbt 2.8 monomer [275]; BPN; 1 acetone and 10 HOHs Subtilisin BPN' (Bacillus amyloliquefaciens and Bacillus subtilis) (2st1: 1cse.E [1thm] [2pkc]) {a/b/a doubly wound para beta ud/ud + c/b open face para beta ud + anti betas + crossed alphas} [sbt+] #1s01 1.7 monomer [275]; M50F, N76D, G169A, Q206C, Y217K, & N218S mutant; residue 206 may be persulfide; 2 IPAs, 1 Ca, and 215 HOHs #1s02 1.9 monomer [275]; Q19E and Q217E mutant; inhibited, but inhibitor not modeled in; 2 Ca, 1 SO4, and 118 HOHs #1sbn 2.1 monomer + L45R mutant Eglin-C inhibitor - 2 chains given [274, 70]; 2 Ca++s and 316 HOHs #1sib 2.4 monomer + inhibitor (a + i) - 2 chains given [275, 70]; mutant inhibitor (I:R53K); 2 Ca++s and 195 HOHs #2sic 1.8 monomer + inhibitor (a + a + i2) - 2 chains given [275, 107]; BPN'; supersedes 1sic; inhibitor is dimer & binds 2 subtilisins; 2 Ca++s and 258 HOHs; 2 SSs #3sic 1.8 monomer + Streptomyces subtilisin inhibitor (a + a + i2) - 2 chains given [275, 107]; BPN'; M73K inhibitor is a dimer & binds 2 subtilisins; 2 Ca++s and 273 HOHs; 2 SSs #5sic 2.2 monomer + Streptomyces subtilisin inhibitor (a + i) - 2 chains given [275, 107]; BPN'; M70G, M73K inhibitor; 2 Ca++s and 288 HOHs; 2 SSs #2sni 2.1 monomer + chymotrypsin inhibitor - 2 chains given [275, 83]; E251Q mutant; 2 Ca++s and 168 HOHs; BPN' #2st1 1.8 monomer [275]; BPN'; 2 Ca++s, 1 SO4, and 154 HOHs #1st2 2.0 monomer [275]; BPN'; peroxide inactivated - 3 mets oxidized; 2 Ca++s, 1 SO4, and 116 HOHs; seq as 2st1 #1sub 1.75 monomer [275]; N218S and S221C mutant; 2 oxygens bound to SGs, 1 Ca++, 1 K+, 1 acetone, and 152 HOHs #1suc 1.80 monomer [266]; M50P, Y217K, N218S, S221C, and DEL(75-83) mutant; BPN'; 2 oxygens bound to CGs, 1 K+, 1 acetone, and 165 HOHs #1sud 1.90 monomer [275]; M50P, Y217K, N218S, S221C mutant; BPN'; 2 oxygens bound to CGs, 2 Ca++s, 1 K+, 1 acetone, and 176 HOHs Subtilisin Carlsberg (Bacillus subtilis and Bacillus licheniformis) (1cse.E: 1cse.E [1thm] [2pkc]) {a/b/a doubly wound para beta ud/ud + anti betas + crossed alpha + alpha} [sbt] XXX Thornton dw1 #1cse 1.2 monomer + inhibitor Eglin-C - 2 chains given [274, 71]; 2 Ca++s and 432 HOHs #1sbc 2.5 monomer [275]; 1 Ca++ #1sca 2.0 monomer [274]; aqueous form; 2 Ca++s, 1 Na+, and 126 HOHs #1scb 2.3 monomer [274]; acetonitrile soaked crystals; 1 Ca++, 12 aceto- nitriles, and 99 HOHs #1scd 2.3 monomer [274]; 2 Ca++s and 114 HOHs; crystals crosslinked with glutaraldehyde #2sec 1.8 monomer + inhibitor N-Acetyl-Eglin-C - 2 chains given [274, 71]; 3 Ca++s and 170 HOHs #1sel 2.0 monomer - 2 chains given [274]; A:221 and B:221 are seleno- cysteines; 2 seleninic acids, 4 Ca++s and 121 HOHs Sulfate Binding Protein (Salmonella typhimurium) (1sbp: 1sbp) {domain 1: 1-94,219-274: a/b/a doubly wound mixed beta ud/ud + para alpha pair} {domain 2: 94-218, 275-309: a/b/c doubly wound anti beta ud/cr + crossed alpha} XXX encircled axial alpha #1sbp 1.7 monomer? [310]; 1 SO4 and 138 HOHs Cu, Zn Superoxide Dismutase (Bos taurus) (2sod.B: 2sod.B) {Greek anti beta} [sod] XXX Thornton Greek 2 #1cob 2.0 dimer (a2) - 2 chains given [151]; 2 Cu++s, 2 Co++s, and 199 HOHs; 2 SSs #1sda 2.5 dimer (a2) - 4 chains given [151]; nitrated at Tyr 108; 4 Zn++s, 4 Cu++s, 4 nitrites, and 4 HOHs; 4 SSs #2sod 2.0 dimer (a2) - 4 chains given [151]; supersedes 1sod; acetylated; 4 Cu++s, 4 Zn++s, and 4 HOHs; 4 SSs #3sod 2.1 dimer (a2) - 1 chain given [151]; C6A mutant; acetylated; 1 Cu++ and 1 Zn++; 1 SS Cu, Zn Superoxide Dismutase (Homo sapiens) (1sos.A: 2sod.B) {Greek anti beta + alpha} [sod+] #1sos 2.5 dimer (a2) - 10 chains given [153]; C6A and C111S mutant; 10 Cu++s, 10 Zn++s, 2 SO4s, and 499 HOHs; 10 SSs Cu, Zn Superoxide Dismutase (Saccharomyces cerevisiae) (1sdy.A: 2sod.B) {Greek anti beta + alpha} [sod+] #1sdy 2.5 tetramer (a4) - 4 chains given [153]; 4 Cu++s, 4 Zn++s, and 513 HOHs; 4 SSs Cu, Zn Superoxide Dismutase (Spinacea oleracea) (1srd.A: 2sod.B) {Greek anti beta} [sod+] XXX 3 loop + strand (bent loops) #1srd 2.0 tetramer? (a4) - 4 chains given [154]; 4 Cu++s, 4 Zn++s, and 104 HOHs; 4 SSs Iron Superoxide Dismutase (Pseudomonas ovalis) (3sdp.A: 3sdp.A [1abm.A] [3mds.A]) {domain 1: 5-84: up down anti alpha pair} {domain 1: 85-191: a/b/c doubly wound anti beta ud/cr + alpha} #3sdp 2.1 dimer (a2) - 2 chains given [195]; 2 Fes and 180 HOHs Mn Superoxide Dismutase (Homo sapiens) (1abm.A: 1abm.A [3sdp.A] [3mds.A]) (domain 1: 1-79: up down anti alpha pair + alpha} {domain 2: 80-198: a/b/a doubly wound anti beta ud/cr + crossed alpha} [[mds]] #1abm 2.2 tetramer (a4) - 2 chains given [198]; 2 Mn++s and 169 HOHs #1msd 3.2 tetramer (a4) - 2 chains given [198]; 2 Mn+++s Mn Superoxide Dismutase (Thermus thermophilus, strain HB8) (3mds.A: 3mds.A [3sdp.A] [1abm.A]) (domain 1: 1-90: up down anti alpha pair + alpha} {domain 2: 91-204: a/b/c doubly wound anti beta ud/ud + crossed alpha} [[mds]] #3mds 1.8 dimer? (a2) - 2 chains given [203]; 2 Mn++s and 187 HOHs TATA Binding Protein (Saccharomyces cerevisiae) (1tbp.A: 1tbp.A) {domain 1: 61-165: a/b open face anti beta cr + alpha} {domain 2: 166-240: a/b open face anti beta cr + alpha} #1tbp 2.6 dimer? (a2) - 2 chains given [180] Telokin (Meleagris gallopavo) (1tlk: 1tlk) {Greek anti beta} 3 loop XXX #1tlk 2.8 monomer? [154]; C-terminal domain of myosin light chain kinase; 31 HOHs Tenascin (Homo sapiens) (1ten: 1ten) {Greek anti beta} #1ten 1.8 fragment [90]; 3rd fibronectin III repeat; 74 HOHs Tetracyclin Repressor (Escherichia coli) {domain 1: 1-47: crossed alpha} {domain 2: 48-208: a/a/a doubly wound para alpha} #2tct 2.1 dimer (a2) - 1 chain given [207]; 1 CTC, 1 Mg++, and 135 HOHs Transcriptional Elongation Factor SII (TFIIS) (Homo sapiens) (1tfi: 1tfi) {metal rich open face anti beta} #1tfi NMR monomer - 12 models given [50]; nucleic-acid binding domain; 1 Zn Yeast Transcription Factor ADR1 (Saccharomyces cerevisiae) (1ard: 1ard [1zaa.C] [1znf]) {a/b open face anti beta} finger+ #1ard NMR fragment - 10 models given [29]; N-terminal domain; 1 Zn++ #1are NMR fragment - 10 models given [29]; N-terminal domain; H118A mutant; 1 Zn++ #1arf NMR fragment - 10 models given [29]; N-terminal domain; H118Y mutant; 1 Zn++ Thaumatin I (Thaumatococcus danielli Benth) (1thi: 1thi) {Greek anti beta} XXX #1thi 3.2 CA monomer [207]; 8 SSs Theiler's Murine Encephalomyelitis Virus Coat Protein (Murine Encephalomyelitis Virus, DA strain) (1tme.1: 1tme.1 [2mev.1]) {Greek anti beta} [virus+] XXX (1tme.2: 1tme.2 [1bbt.2] [2plv.2]) {Greek anti beta} [virus+] (1tme.3: 1tme.3 [1bbt.3] [4rhv.3] [2plv.3]) {Greek anti beta} [virus+] (1tme.4: 1bbt.4) {coil} #1tme 2.8 240mer (60abcd) - 4 chains given [274, 267, 236, 71]; DA strain; 327 HOHs Theiler's Murine Encephalomyelitis Virus Coat Protein (Murine Encephalomyelitis Virus, bean strain) (1tmf.1: 1tme.1 [2mev.1]) XXX {Greek anti beta} [virus+] (1tmf.2: 1tme.2 [1bbt.2] [2plv.2]) {Greek anti beta} [virus+] (1tmf.3: 1tme.3 [1bbt.3] [4rhv.3] [2plv.3]) {Greek anti beta} [virus+] (1tmf.4: 1bbt.4) {coil} #1tmf 3.5 240mer (60abcd) - 4 chains given [274, 267, 232, 31]; bean strain; 1 SS Thermitase (Thermoactinomyces vulgaris) (1thm: 1thm [1cse.E] [2pkc]) {a/b/a doubly wound para beta ud/ud + anti beta + alphas} [sbt] XXX #1tec 2.2 monomer + inhibitor Eglin C [279, 70]; 2 Ca++s, 1 Na+, and 208 HOHs #2tec 1.98 monomer + inhibitor Eglin C [279, 70]; residue 199 may be a W; 5 mM Ca; 2 Ca++s, 1 Na+, and 224 HOHs #3tec 2.0 monomer + inhibitor Eglin C [279, 70]; residue 199 may be a W; 100 mM Ca; 3 Ca++s and 130 HOHs #1thm 1.37 monomer [279]; 2 Ca++s, 1 Na+, 3 SO4s, and 193 HOHs Thermolysin (Bacillus thermoproteolyticus) (8tln: 8tln [1ezm]) {domain 1: 1-152: a/b/c doubly wound mixed beta ud/cr + anti beta} {domain 2: 153-316: crossed + schief alpha} or {domain 1: 1-126: XXX {domain 2: 127-234: XXX {domain 3: 235-316: a/a/a doubly wound para beta ud/cr + anti beta} [tln] #1thl 1.7 monomer [316]; 1 N-(1-(2(R,S)-carboxy-4-phenylbutyl) cyclopentyl- carbonyl)-(S)-tryptophan, 1 Ca++, 1 Zn++, and 148 HOHs #4tln 2.3 monomer [316]; 1 L-leucyl-hydroxylamine, 4 Ca++s, 1 Zn++, and 150 HOHs #5tln 2.3 monomer [316]; 1 HONH-benzylmalonyl-L-alanylglycine-p-nitro- anilide, 4 Ca++s, 1 Zn++, and 146 HOHs #7tln 2.3 monomer [316]; supersedes 6tln; 1 CH2CO(N-OH)leu-OCH3, 4 Ca++s, 1 Zn++, and 166 HOHs #8tln 1.60 monomer + peptide - 2 chains given [316, 2]; supersedes 3tln; 4 Ca++s, 1 Zn++, 1 DMS, and 157 HOHs #1tlp 2.3 monomer + inhibitor - 2 chains given [316, 3]; 4 Ca++s, 1 Zn++, 1 alpha-L-rhamnopyranosyloxyhydroxyphosphinyl, and 163 HOHs #1tmn 1.9 monomer + peptide - 2 chains given [316, 3]; 1 1-carboxy-3- phenyl-propyl, 4 Ca++s, 1 Zn++, and 144 HOHs #2tmn 1.6 monomer + peptide - 2 chains given [316, 2]; 1 phosphate, 4 Ca++s, 1 Zn++, 1 terminal amide, and 168 HOHs #3tmn 1.7 monomer + peptide - 2 chains given [316, 2]; 4 Ca++s, 1 Zn++, and 173 HOHs #4tmn 1.7 monomer + peptide - 2 chains given [316, 4]; 1 carbobenzoxy, 4 Ca++s, 1 Zn++, 1 modified Gly with C=0 replaced by PO2, and 162 HOHs #5tmn 1.6 monomer + peptide - 2 chains given [316, 4]; 1 carbobenzoxy, 4 Ca++s, 1 Zn++, 1 modified Gly with C=0 replaced by PO2, and 174 HOHs #6tmn 1.6 monomer + peptide - 2 chains given [316, 4]; 1 carbobenzoxy, 1 modified Gly with C=0 replaced by PO2, 1 modified Leu with N replaced by O, 4 Ca++s, 1 Zn++, and 170 HOHs #7tmn --- monomer model of substrate [4]; 1 phe with tetrahedral carbonyl carbon Gamma-1-P Thionin (Triticum turgidum) (1gps: 1gps) {SS rich a/b open face anti beta cr} #1gps NMR monomer - 8 models given [47]; 4 SSs Gamma-1-H Thionin (Triticum turgidum) (1gpt: 1gps) {SS rich a/b open face anti beta cr} #1gpt NMR monomer - 8 models given [47]; 4 SSs Thioredoxin (Escherichia coli B) (2trx.A: 2trx.A [3trx]) {a/b/a doubly wound mixed beta ud/ud+cr} XXX Thornton dw1 #1srx 2.8 CA monomer [108]; oxidized; 4 res differ from 1trx and 2trx; 1 SS #1tho 2.3 monomer [109]; Ins(33R34) mutant; 1 Cu++ and 26 HOHs; 1 SS #2tir 2.0 monomer [108]; K36E mutant; 1 Cu++ and 80 HOHs; 1 SS #1trx NMR monomer - 10 models given [108]; reduced #2trx 1.68 monomer - 2 chains given [108]; 2 Cu++s, 8 2-methyl-2,4-pentane- diols, and 140 HOHs; 2 SSs Thioredoxin (Homo sapiens) (3trx: 3trx [2trx.A]) {a/b/a doubly wound mixed beta ud/cr} #3trx NMR monomer [105]; reduced; minimized average structure #4trx NMR monomer - 33 models given [105]; reduced Thioredoxin Reductase (Homo sapiens) (1trb: 1trb) {domain 1: 1-117,245-316: a/b/b doubly wound para beta ud/ud} XXX {domain 2: 245-316: a/b/b doubly wound para beta ud/cr} #1trb 2.0 monomer [320]; C138S mutant; 1 FAD and 164 HOHs Thrombin (Bos taurus) (1iht.H: 1ppb.H [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [3rp2.A] [1ton] [1sgt] [1hne.E]) {domain 1: Greek anti beta} XXX see 1ppb {domain 2: Greek anti beta} #1bbr 2.3 monomer + peptide - 10 chains given [49, 150, 109, 11, 49, 259, 11, 49, 259, 11]; 3 complexes - first has epsilon-thrombin [3 chains], others are alpha-thrombin [2 chains]; each thrombin has bound fibrinopeptide I; 706 HOHs; 12 SSs #1etr 2.2 monomer (cleaved ab) + inhibitor - 3 chains given [49, 259, 3]; 1 (2R,4R)-4-methyl-1-[nalpha-(IRS)-3-methyl-1,2,3,4-tetrahydro- 8-quinolinesulfonyl)-L-arginyl]-2-piperdine carboxylic acid and 152 HOHs; 4 SSs #1ets 2.3 monomer (cleaved ab) + inhibitor - 3 chains given [49, 259, 4]; 1 nalpha-(2-naphthyl-sulfonyl-glycyl)-DL-amidino-phenylalanyl- piperdine and 228 HOHs; 4 SSs #1ett 2.5 monomer (cleaved ab) + inhibitor - 3 chains given [49, 259, 3]; 1 nalpha-(4-toluene-sulfonyl)-DL-m-amidino-phenylalanyl-piperdine and 180 HOHs; 4 SSs #1hrt 2.8 monomer (cleaved, LH) + hirudin inhibitor - 3 chains given [49, 259, 65]; variant 1; 129 HOHs; 7 SSs #1ihs 2.0 monomer (cleaved, LH) + hirutonin-2 - 3 chains given [36, 259, 22]; 1 propanal link from I:R3 to I:Q49 and 146 HOHs; 4 SSs #1iht 2.0 monomer (cleaved, LH) + hirutonin-6 - 3 chains given [36, 259, 14]; 1 propanal link from I:R3 to I:FBE4, 2 1-formyl-4-amino-2,3- butene (FBE) and 168 HOHs; 4 SSs Calcium Prothrombin (Bos taurus) (2pf1: 2pf1 [1kdu] [1tpk.A] [1pk4] [2hpp.P]) {misc anti beta + anti alpha} XXX (2hpp.P: 2hpp.P [1kdu] [1tpk.A] [1pk4] [2pf1]) {SS rich anti beta + coil} DUP2hpp 3.3 fragment + HS thrombin (ab) + inhibitor - 4 chains given [79, 36, 259, 4]; prothrombin fragment 2; 1 methylene and 119 HOHs; 6 SSs #2pf1 2.2 fragment [156]; prothrombin fragment 1; 164 HOHs; 4 SSs #2pf2 2.2 fragment [145]; prothrombin fragment 1; 10 gamma-carboxy-glutamic acids, 7 Ca++s, and 144 HOHs; 5 SSs Prothrombin (Homo sapiens) (2hpq.P: 2hpp.P [1kdu] [1tpk.A] [1pk4] [2pf1]) {SS rich anti beta + coil} DUP2hpq 3.3 peptide + alpha-thrombin (cleaved, LH) + inhibitor - 4 chains given [79, 36, 259, 4]; 1 methylene and 122 HOHs; 7 SSs Alpha-Thrombin (Homo sapiens) (1ppb.H: 1ppb.H [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [3rp2.A] [1ton] [1sgt] [1hne.E]) (1ppb.L: 1ppb.L) {domain 1: Greek anti beta} + alphas XXX {domain 2: Greek anti beta} [s_prot+] #1abi 2.3 monomer (cleaved, LH) + hirulog 3 [36, 259, 20]; 1 beta-homo- arginine, 1 D-phenylalanine, and 246 HOHs; 4 SSs #1abj 2.4 monomer (cleaved, LH) + peptide [36, 259, 4]; peptide is D-phe- pro-arg chloromethylketone, PPack; 1 methylene and 196 HOHs; 4 SSs #1dwb 3.18 dimer (ab) + hirudin peptide [36, 259, 11]; 1 benzamidine and 50 HOHs; 4 SSs #1dwc 3.0 dimer (ab) + hirudin peptide [36, 259, 11]; 1MD-805 and 50 HOHs; 4 SSs #1dwd 3.0 dimer (ab) + hirudin peptide [36, 259, 11]; 1 N==alpha==-(2- naphthyl-sulfonyl-glycyyl)-(DL)-para-amidinophenylalanyl-piperi- dine and 50 HOHs ; 4 SSs #1dwe 3.0 dimer (ab) + hirudin peptide + inhibitor [36, 259, 11, 4]; 1 D- Phe-Pro-Arg-chloromethylketone, 1 methylene, and 55 HOHs; 4 SSs #1fph 2.5 monomer (cleaved, LH) + hirudin + fibrinopeptide - 4 chains given [36, 259, 12, 12]; 1 methylene and 168 HOHs; 4 SSs #2hat 2.5 monomer (cleaved, LH) + hirugen + FHAM - 4 chains given [36, 259, 10, 6]; 1 sulfonate bound to I:Y63, 1 methyl benzene, 1 amido benzene, 1 fused ring fragment, 1 methyl group, and 172 HOHs; 4 SSs #1hgt 2.2 monomer (cleaved, LH) + hirugen - 3 chains given [36, 259, 13]; 1 sulfonate and 243 HOHs; 4 SSs #2hgt 2.2 monomer (cleaved, LH) + hirulog I (cleaved, IJ) [36, 259, 3, 17]; 222 HOHs; 4 SSs; 4 SSs #3htc 2.3 CA monomer (cleaved, LH) + hirudin variant 2 - 3 chains given [36, 259, 65]; hirudin: variant 2, K47; 7 SSs #4htc 2.3 monomer (cleaved, LH) + hirudin variant 2 - 3 chains given [36, 259, 65]; hirudin: variant 2, K47; 1 NAG and 262 HOHs; 7 SSs #2hpp 3.3 monomer (cleaved, LH) + inhibitor + bovine prothrombin peptide - 4 chains given [36, 259, 4, 79]; 1 methylene and 119 HOHs; 6 SSs #2hpq 3.3 monomer (cleaved, LH) + inhibitor + human prothrombin peptide - 4 chains given [36, 259, 4, 79]; 1 methylene and 122 HOHs; 7 SSs #1ppb 1.9 monomer (cleaved, LH) + peptide - 3 chains given [36, 259, 3]; 1 D-Phe-Pro-Arg, 1 methylene, and 409 HOHs; 4 SSs #1thr 2.3 monomer (cleaved, LH) + hirullin - 3 chains given [36, 259, 13]; 190 HOHs; 4 SSs #1ths 2.2 monomer (cleaved, LH) + inhibitor MDL-28050 - 3 chains given [36, 259, 11]; 1 succinic acid, 1 cyclohexane bonded to I:Ala64, and 190 HOHs; 4 SSs #1tmb 2.3 monomer (cleaved, LH) + hirugen + inhibitor - 4 chains given [36, 259, 13, 7]; 1 2-amino-2hydroxyethyl-tyrosine, 1 sulfonate bound to I:Y63, and 239 HOHs; 4 SSs Thymidine Phosphorylase (Escherichia coli K12) (1tpt: 1tpt) {domain 1: 1-67,155-192: single stranded alpha cylinder} {domain 2: 68-154,193-329: a/b/a doubly wound para beta ud/ud + wedge alpha + alphas} {domain 3: a/b/open face anti beta ud + anti beta} #1tpt 2.8 CA dimer - 1 chain given [440]; 1 SO4 and 1 thymine Thymidylate Synthase (Escherichia coli) (2tsc.A: 2tsc.A) {a/b open face anti beta cr + up down anti alphas + anti betas} #2bbq 2.3 dimer (a2) - 2 chains given [264]; 2 UMPs, 2 10-parpargyl-5,8-di- deazafolate-4(GLU) and 104 HOHs #2tsc 1.97 dimer (a2) - 2 chains given [264]; 2 UMPs, 2 10-propargyl-5,8-di- deazafolate, and 198 HOHs #3tms 2.1 dimer (a2) - 1 chain given [264]; 1 phosphate and 11 HOHs; 1 residue differs from 2tsc Thymidylate Synthase (Lactobacillus casei) (4tms: 2tsc.A) {domain 1: 1-69,142-316: a/b open face anti beta cr + up down anti alphas + anti betas} {domain 2: 70-141: crossed alpha} partially encircled axial helix #1tda 3.09 dimer? - 1 chain given [316]; V316- deletion mutant; 1 phosphate and 37 HOHs #1tdb 2.65 dimer? - 1 chain given [316]; V316- deletion mutant; 1 5-fluoro UMP and 41 HOHs #1tdc 2.65 dimer? - 1 chain given [316]; V316- deletion mutant; 1 UMP #2tdd 2.7 dimer? - 1 chain given [316]; V316- deletion mutant; 1 5-fluoro UMP and 1 5-hydroxymethylene tetrahydrofolate, and 9 HOHs #1tdm 2.55 monomer? [316]; 1 UMP and 33 HOHs #1thy 2.9 dimer? - 1 chain given [316]; form I crystals; 1 UMP and 30 HOHs #4tms 2.35 dimer? - 1 chain given [316]; 1 phosphate and 39 HOHs Tobacco Mosaic Virus (TMV vulgare strain) (2tmv.P: 2tmv.P) {up down anti alpha + anti beta + coil} [tmv] #2tmv 2.9 2130mer (a2130) - 1 chain given [158]; 1 RNA [GAA]; 1 Ca and 74 HOHs Tomato Bushy Stunt Virus (TBSV) (2tbv.A: 2tbv.A) {domain 1: 101-271: double stranded beta cylinder + alpha} {domain 2: 272-387: double stranded beta cylinder} [virus] #2tbv 2.9 180mer (a180) - 3 chains given [387]; 6 Ca+s Tonin (Rattus rattus) (1ton: 1ton [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1hne.E] [1sgt]) {domain 1: 16-128,232-246: Greek anti beta + alpha} {domain 2: 129-231: Greek anti beta} [s_prot] #1ton 1.8 monomer [235]; 1 Zn++ and 149 HOHs; 5 SSs Delta-Toxin or Delta Hemolysin (Staphylococcus aureus and Synthetic) (2dtb: 2dtb) {alpha} (1dhl.A: 1dhl.A) #1dhl --- dimer (a2) - 2 chains given [26]; non-experimental model #2dhl --- dimer (a2) - 2 chains given [26]; non-experimental model #3dhl --- dimer (a2) - 2 chains given [26]; non-experimental model #1dtc NMR monomer? - 12 models given [27]; acetylated #2dtb NMR monomer? - 9 models given [26] Toxin Alpha (Naja nigricollis) (1nea: 3ebx [1cdt.A] [1nbt.A] [2abx.A] [2ctx] [1fas]) {SS rich open face anti beta + anti beta} [tox+] #1nea NMR monomer? - 8 models given [61]; 4 SSs Transcription Factor LFB1 (Rattus rattus) (1lfb: 1lfb) {a/a open face anti alpha cr} #1lfb 2.8 monomer? [99]; homeodomain Transfer RNA Asp (Saccharomyces cerevisiae) #2tra 3.0 monomer [75]; A form: no res 47; 1 spermine, 1 Mg++, and 88 HOHs #3tra 3.0 monomer [75]; supersedes 9tna; B form: no res 47 Transfer RNA Gln (Escherichia coli) DUP1gsg 2.8 CA tRNA + synthetase (s + a) - 2 chains given [75, 553] Transfer RNA Phe (Saccharomyces cerevisiae) #1tn1 3.0 monomer [76]; pH 7.4; 3 Pb++s; no coordinates except for Pbs #1tn2 3.0 monomer [76]; pH 5.0; 3 Pb++s, 1 spermine, 5 Mg++s, and 108 HOHs #4tna 2.5 monomer [76]; supersedes 3tna; 1 Y-base and 4 Mg++s #6tna 2.7 monomer [76]; supersedes 5tna; 1 Y-base, 4 Mg++s and 64 HOHs #1tra 3.0 monomer [76]; supersedes 8tna; 1 Y-base, 5 Mg++s and 110 HOHs #4tra 2.7 monomer [76]; 1 Y-base, 4 Mg++s and 104 HOHs Transfer RNA Ser (Saccharomyces cerevisiae) #5tra --- monomer [85]; theoretical model Transferrin (Oryctolagus cuniculus) (1tfd: 1lfg [1ovb]) {domain 1: 6-92,248-304: a/b/a doubly wound anti beta cr/cr + anti beta + alphas} {domain 2: 93-247: a/b/a doubly wound para beta ud/ud + a/b/a doubly wound anti beta ud/ud} #1tfd 2.3 monomer [304]; N-terminal half; 1 CO3-- and Fe+++; 7 SSs Transforming Growth Factor Alpha (Homo sapiens) (2tgf: 2tgf) {SS rich anti beta} #2tgf NMR monomer [50]; minimized average structure; 3 SSs #3tgf NMR monomer - 4 models given [50]; 3 SSs #4tgf NMR monomer - 4 models given [50]; des-Val1-DesVal2; pH 6.3 and 20 degrees C; first two (missing) residues are modeled in; 3 SSs Transforming Growth Factor Beta 2 (Homo sapiens) (2tgi: 2tgi) {SS rich anti beta + alpha} #1tfg 1.95 monomer? [112]; 2 monomers? linked by disulfide; 84 HOHs; 4 SSs #2tgi 1.8 dimer (a2) - 1 chain given [112]; 58 HOHs; 4 SSs Transthyretin (Prealbumin) (Homo sapiens) (2pab.A: 2pab.A) {Greek anti beta + alpha} [pab] XXX Thornton Greek 2 #2pab 1.8 tetramer (a4) - 2 chains given [127]; supersedes 1pab #1tha 2.0 tetramer (a4) - 2 chains given [127]; 2 3',3'-diiodo-L-thyronines and 98 HOHs #1thc 2.3 tetramer (a4) - 2 chains given [127]; 1 3',5'-dibromo-2',4,4',6- tetra-hydroxyaurone and 95 HOHs #1tlm 1.9 tetramer (a4) - 2 chains given [127]; 2 milrinones and 130 HOHs #1tta 1.7 tetramer (a4) - 2 chains given [127]; 184 HOHs #1ttb 1.7 tetramer (a4) - 2 chains given [127]; A109T mutant; 175 HOHs #1ttc 1.7 tetramer (a4) - 2 chains given [127]; V30M mutant; 319 HOHs Triacylglycerol Acylhydrolase (Rhizomucor miehei) (3tgl: 3tgl) {a/b/a doubly wound para beta ud/cr + anti betas + alpha} #1tgl 1.9 CA monomer [269]; 3 SSs #3tgl 1.9 monomer [269]; 230 HOHs; 3 SSs #4tgl 2.6 monomer [269]; 1 diethylphosphate and 238 HOHs; 3 SSs #5tgl 1.9 CA monomer [269]; T269S variant; N-hexylphosphonate ethyl ester; 3 SSs Trimethylamine Dehydrogenase (Methylotrophic bacterium W3A1) (2tmd.A: 2tmd.A) {domain 1: 1-380: a/b singly wound para beta} [barrel+] {domain 2: 381-488,649-729: a/b/a doubly wound para beta ud/ud} {domain 3: 489-648: a/b/b doubly wound para beta ud + anti beta + alpha} #2tmd 2.4 monomer - 2 chains given [729]; 2 Fe4S4s, 2 FMNs, 2 ADPs, and 581 HOHs Triose Phosphate Isomerase (Escherichia coli) (1tre.A: 1ypi.A) {a/b singly wound para beta} [barrel+] #1tre 2.6 dimer (a2) - 2 chains given [255]; 172 HOHs Triose Phosphate Isomerase (Gallus gallus) (1tim.A: 1ypi.A) {a/b singly wound para beta} [barrel] #1tim 2.5 dimer (a2) - 2 chains given [247] Triose Phosphate Isomerase (Trypanosoma brucei brucei) (5tim.A: 1ypi.A) {a/b singly wound para beta + anti beta + alpha} [barrel+] #3tim 2.8 dimer (a2) - 2 chains given [250]; SO4 removed; 30 HOHs #4tim 2.4 dimer (a2) - 2 chains given [250]; chain A "open"; chain B "closed"; 1 2-phosphoglycerate and 130 HOHs #5tim 1.83 dimer (a2) - 2 chains given [250]; supersedes 2tim; chain A "open"; chain B "closed"; 2 SO4s, 1 oxidized dithiothreitol, and 279 HOHs #6tim 2.2 dimer (a2) - 2 chains given [250]; chain A "open"; chain B "closed"; 1 glycerol-3-phosphate, and 91 HOHs #1trd 2.5 dimer (a2) - 2 chains given [250]; each chain from different dimer; different crystal form; 1 phosphoglycolohydroxamate and 61 HOHs #1tsi 2.84 dimer (a2) - 2 chains given [250]; 1 N-hydroxy-4-phosphono-butan- amide and 53 HOHs Triose Phosphate Isomerase (Saccharomyces cerevisiae) (1ypi.A: 1ypi.A) {a/b singly wound para beta} [barrel] #7tim 1.9 dimer (a2) - 2 chains given [247]; 2 phosphoglycolohydroxamates and 247 HOHs #1ypi 1.9 dimer (a2) - 2 chains given [247]; 119 HOHs #2ypi 2.5 dimer (a2) - 2 chains given [247]; 2 2-phosphoglycolates and 25 HOHs #3ypi 2.8 dimer (a2) - 2 chains given [247]; H95Q mutant; 2 phosphoglyco- hydroxamates Tropomyosin (Oryctolagus cuniculus) (2tma.A: 2tma.A) {alpha} #2tma 15.0 CA dimer? (a2) - 2 chains given [284] Troponin (Oryctolagus cuniculus) (1tnc: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 14-90: crossed alpha + anti beta} {domain 2: 91-157: crossed alpha + anti beta} [ca_bind+] #1tnc --- monomer? [146]; non-experimental; based on parvalbumin; 4 Ca++s Troponin C (Gallus gallus) (4tnc: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 3-91: crossed alpha + anti beta} {domain 2: 92-162: crossed alpha + anti beta} [ca_bind] #1cta NMR fragment dimer (a2) - 2 chains given [36]; minimized average structure; site III only; 2 terminal amides and 2 Ca++s #1ctd NMR fragment dimer (a2) - 7 models of 2 chains each given [36]; site III only; 2 terminal amides and 2 Ca++s #4tnc 2.0 monomer [162]; supersedes 3tnc; 2 Ca++s; extended form #1top 1.78 monomer? [163]; 2 Ca++s, 1 SO4, and 164 HOHs; extended form Troponin C (Meleagris gallopavo) (5tnc: 1osa [2sas] [4icb] [1rro] [4cpv] [1rec]) {domain 1: 2-110: crossed alpha + anti beta} {domain 2: 111-162: crossed alpha + anti beta} [ca_bind] #5tnc 2.0 monomer [162]; supersedes 2tnc; 2 Ca++s and 157 HOHs; extended form Trypanothione Oxidoreductase (Crithidia fasciculata) (2tpr.A: 2tpr.A [1npx] [3grs] [3lad.A] [1lvl]) {domain 1: 1-173,286-358: a/b/b doubly wound para beta ud + anti betas} {domain 2: 165-285: a/b/b doubly wound para beta ud} {domain 3: 359-482: a/b/a doubly wound anti beta ud/ud} #2tpr 2.4 dimer (a2) - 2 chains given [490]; 2 FADs and 350 HOHs; 2 SSs #1typ 2.8 dimer (a2) - 2 chains given [487]; 2 FADs, 2 NAP+s, 4 gluta- thiones, 4 spermidines, and 400 HOHs; 2 SSs Trypsin Beta (Bos taurus) (1tgn: 1tgn [2cga.A] [3est] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: 17-120,232-245: Greek anti beta + alpha} {domain 2: 121-231: Greek anti beta + alpha} [s_prot] XXX Thornton Greek #1gbt 2.0 monomer [223]; 1 guanidinobenzoyl group at Ser 195, 1 Ca++, 2 SO4s, and 117 HOHs; 6 SSs #1ntp 1.8 monomer [223]; N48D, N95D, N115D chemically modified; monoisopro- pylphosphoryl inhibited; neutron data; 6 SSs #1ppc 1.8 monomer + inhibitor - 2 chains given [223, 4]; 1 [N==alpha==-(2- naphthyl-sulfonyl-glycyl)-DL-P-amidinophenylalanyl-piperidine], 1 Ca++, and 147 HOHs; 6 SSs HOHs; 9 SSs #1ppe 2.0 monomer + inhibitor CMTI-I - 2 chains given [223, 29]; 140 #1pph 1.9 monomer + inhibitor [223, 3]; 1 3-TAPAP, 1 Ca++, 1 SO4, and 214 HOHs; 6 SSs #3ptb 1.7 monomer [223]; pH 7; supersedes 2ptb; 1 benzamidine, 1 Ca++ and 62 HOHs; 6 SSs #2ptc 1.9 monomer + inhibitor PTI - 2 chains given [223, 58]; supersedes 1ptc; 1 Ca++ and 157 HOHs; 9 SSs #2ptn 1.55 monomer [223]; orthorhombic crystal; supersedes 1ptn; 2.4 M ammonium sulfate; 1 Ca++ and 82 HOHs; 6 SSs #3ptn 1.7 monomer [223]; trigonal; 2.4 M ammonium sulfate; 1 Ca++ and 82 HOHs; 6 SSs #4ptp 1.34 monomer [223]; supersedes 3ptp; diisopropylphosphoryl derivative of S195; 1 Ca++ and 168 HOHs; 6 SSs #1tab 2.3 monomer + inhibitor - 2 chains given [223, 82]; 1 Bowman-Birk inhibitor; much of density for inhibitor is missing; 140 HOHs; 10 SSs #2tga 1.8 monomer [229]; zymogen; supersedes 1tga; 2.4 M MgSulfate; 1 Ca++ and 93 HOHs; 6 SSs #1tgb 1.8 monomer [229]; zymogen; CA form; trypsinogen; 1 Ca++ and 120 HOHs; 6 SSs #1tgc 1.8 monomer [229]; zymogen; 50% methanol 50% HOH; 1 Ca++ and 93 HOHs; 6 SSs #2tgd 2.1 monomer [229]; zymogen; inhibitor linked to S195, 1 Ca++, and 73 HOHs; 6 SSs #1tgn 1.65 monomer [229]; zymogen; 6 SSs #2tgp 1.9 monomer + BPTI inhibitor - 2 chains [229, 58]; zymogen; super- sedes 1tgp; 1 Ca++, 1 SO4, and 138 HOHs; 9 SSs #1tgs 1.8 monomer + pancreatic secretory trypsin inhibitor - 2 chains [229, 56]; zymogen; 1 Ca++, 1 SO4, and 152 HOHs; 9 SSs #1tgt 1.7 monomer [229]; zymogen; 173 degrees K; 1 Ca++, 2 methanols, and 123 HOHs; 6 SSs #2tgt 1.7 monomer [229]; zymogen; 103 degrees K; 70:30 = methanol:HOH; 1 Ca++, 2 methanols, and 137 HOHs; 6 SSs; 6 SSs #1tld 1.5 monomer [223]; beta; pH 5.3; 1 Ca++, 1 SO4, and 25 HOHs; 6 SSs #2tld 2.6 monomer + SSI inhibitor (a + 1/2 i2) - 2 chains given [223, 110]; DEL(1-6), K176G, Q205K, K206N, N206K diff with 1tgn; inhibitor is a dimer & binds 2 trypsins; 8 SSs #2tpi 2.1 monomer + inhibitor + substrate - 3 chains [229, 59, 2]; zymogen; 2.4 MgSulfate; inhibitor acetylated; 1 Hg and 139 HOHs; 8 SSs #3tpi 1.9 monomer + PTI inhibitor + Ile-Val substrate [229, 58, 2]; zymo- gen; supersedes 1tpi; 1 Ca++, 2 SO4s, and 152 HOHs; 9 SSs #4tpi 2.2 monomer + PTI-analog inhibitor + Val-Val substrate [229, 58, 2]; zymogen; 1 Ca+, 2 SO4s, and 155 HOHs; 9 SSs #1tpa 1.9 monomer + BPTI inhibitor [223, 58]; anhydro; 1 Ca++ and 159 HOHs; 9 SSs #1tpo 1.7 monomer [223]; beta; pH 5.0; 1 Ca++ and 84 HOHs; 6 SSs #1tpp 1.4 monomer [223]; 1 p-amidino-phenyl-pyruvate, 1 Ca++, 1 SO4, and 93 HOHs; 6 SSs Trypsin (Rattus rattus) (1trm.A: 1tgn [2cga.A] [3est] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1sgt] [1hne.E]) {domain 1: 16-120,232-245: Greek anti beta + alpha} {domain 2: 121-231: Greek anti beta + alpha} [s_prot] #1bra 2.2 monomer [223]; D189G, G226D variant; 1 BEN, 1 Ca++, and 137 HOHs #1brb 2.1 monomer + inhibitor BPTI [223, 58]; D189G, G226D variant; inhibitor variant; 142 HOHs #1brc 2.5 monomer + inhibitor APPI [223, 56]; D189G, G226D variant; inhibitor variant; 141 HOHs #1trm 2.3 monomer - 2 chains given [223]; D102N mutant; B chain more like native; pH 6; 2 benzamidines, 2 Ca++s, and 230 HOHs; 12 SSs #2trm 2.8 monomer [223]; D102N mutant; pH 8; 1 benzamidine, 1 Ca++, and 122 HOHs; 6 SSs Trypsin (Salmo salar) (1tbs: 1tgn [2cga.A] [3est] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: 16-120,235-243: Greek anti beta + alpha} {domain 2: 121-234: Greek anti beta + alpha} [s_prot+] #1bit 1.83 monomer [237]; 2 BENs, 1 Ca++, 1 SO4, and 125 HOHs; 6 SSs #1tbs 1.8 monomer [221]; 1 BEN, 1 Ca++, and 177 HOHs; 6 SSs Trypsin (Streptomyces griseus, strain K1) (1sgt: 1sgt [2cga.A] [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E]) {domain 1: 16-128,232-246: Greek anti beta + alpha} {domain 2: 129-231: Greek anti beta + alpha} [s_prot] XXX Thornton Greek #1sgt 1.7 monomer [223]; 1 Ca++ and 192 HOHs; 3 SSs Trypsin (Sus scrofa) (1mct.A: 1tgn [2cga.A] [3est] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: 16-121,232-245: Greek anti beta + alpha} {domain 2: 122-231: Greek anti beta + alpha} [s_prot+] #1mct 1.6 monomer + inhibitor - 2 chains given [223, 28]; 1 Ca++ and 135 HOHs; 9 SSs Basic Pancreatic Trypsin Inhibitor (Bos taurus) (9pti: 9pti [1aap.A] [1dtx]) {SS rich a/b open face anti beta ud + coil} [pti] #1aal 1.6 monomer - 2 chains given [58]; C30V and C51A mutant; 1 inorganic phosphate group and 126 HOHs; 4 SSs #1bpt 2.0 monomer [58]; Y23A mutant; 1 phosphate and 40 HOHs; 3 SSs DUP1brb 2.1 monomer + trypsin [58, 223]; C5A, C55A variant; trypsin variant; 142 HOHs #1bti 2.2 monomer [58]; F22A mutant; 58 HOHs; 3 SSs #1fan 1.9 monomer [58]; F45A mutant; 56 HOHs; 3 SSs DUP2kai 2.5 inhibitor + Kallikrein monomer (cleaved, ab) - 3 chains given [58, 80, 152]; 10 HOHs; 8 SSs #1nag 1.9 monomer [56]; N43G mutant; 1 phosphate group and 64 HOHs; 3 SSs #1pit NMR monomer - 20 models given [58]; 3 SSs DUP2ptc 1.9 monomer + trypsin protease - 2 chains given [58, 223]; supersedes 1ptc; 1 Ca++ and 157 HOHs; 9 SSs #4pti 1.5 monomer [58]; supersedes 3pti; 60 HOHs; 3 SSs #5pti 1.0/1.8monomer [58]; joint x-ray & neutron; crystal form II; 1 phosphate and 63 deuterated HOHs; 3 SSs #6pti 1.7 monomer [58]; crystal form III; 1 phosphate and 73 HOHs; 3 SSs #7pti 1.6 monomer [58]; C30A, C51A mutant; 1 phosphate and 58 HOHs; 2 SSs #8pti 1.8 monomer [58]; Y35G mutant; 70 HOHs; 3 SSs #9pti 1.22 monomer [58]; M52 oxidized; error in SEQRES records - residue omitted near C terminus; 1 phosphate and 67 HOHs; 3 SSs DUP2tgp 1.9 monomer + trypsinogen protease - 2 chains [58, 229]; supersedes 1tgp; 1 Ca++, 1 SO4, and 138 HOHs; 9 SSs DUP1tpa 1.9 monomer + trypsin protease [58, 223]; anhydro; 1 Ca++ and 159 HOHs; 9 SSs DUP2tpi 2.1 monomer + trypsinogen + substrate - 3 chains [229, 59, 2]; 2.4 MgSulfate; inhibitor acetylated; 1 Hg and 139 HOHs; 8 SSs DUP3tpi 1.9 monomer + trypsinogen protease + Ile-Val substrate [229, 58, 2]; supersedes 1tpi; 1 Ca++, 2 SO4s, and 152 HOHs; 9 SSs DUP4tpi 2.2 monomer + trypsinogen protease + substrate [229, 58, 2]; K15R variant; 1 Ca+, 2 SO4s, and 155 HOHs; 9 SSs Trypsin Inhibitor (Ascaris lumbricoides, variant Suum) {domain 1: 1-39: a/b/b doubly wound anti beta ud/ud} XXX {domain 2: 40-62: c/b/c doubly wound ant beta ud/ud} #1ata NMR monomer [62]; ph 4.75; energy minimized average structure; 5 SSs #1atb NMR monomer [62]; ph 2.4; energy minimized average structure; 5 SSs #1atd NMR monomer - 32 models given [62]; ph 4.75; 5 SSs #1ate NMR monomer - 32 models given [62]; ph 2.4; 5 SSs Trypsin Inhibitor (Curcurbita maxima and Curcurbita ficifolia) (1cti: 1cti) {SS rich anti beta + coil} #1cti NMR monomer [29]; average structure; 3 SSs #2cti NMR monomer - 5 models given [29]; 3 SSs #3cti NMR monomer - 6 models given [29]; 3 SSs DUP1ppe 2.0 monomer + trypsin [29, 223]; 140 HOHs; 9 SSs Trypsin Inhibitor (Momordica charantia, linn. cucurbitaceae) (1mct.I: 1cti) {SS rich anti beta + coil} DUP1mct 1.6 monomer + protease - 2 chains given [28, 223]; 1 Ca++ and 135 HOHs; 9 SSs Trypsin Inhibitor (Stichodactyla helianthus) (1shp: 1aap.A [9pti] [1dtx]) {SS rich a/b open face anti beta ud + coil} see dtx, dtk? #1shp NMR monomer - 20 models given [55]; 3 SSs each Trypsin Inhibitor II (Ecballium elaterium) (2eti: 1cti) {SS rich anti beta + coil} XXX look again #2eti NMR monomer [28]; 3 SSs Trypsin Inhibitor Kunitz DE-3 (Erythrina caffra) (1tie: 1tie) {6 anti beta pairs on cube faces} crossed XXX #1tie 2.5 monomer [172]; 61 HOHs; 2 SSs Mast Cell Tryptase (Homo sapiens) (1aao: 2cga.A [3est] [1tgn] [1hf1] [2cp1] [1ppb.H] [3rp2.A] [1ton] [1hne.E] [1sgt]) {domain 1: 1-115,231-245: Greek anti beta + alpha} {domain 2: 116-230: Greek anti beta + alpha} [s_prot+] #1aao --- monomer [245]; non-experimental model, based on homology to tryp- sin (2ptn); 4 SSs TRP Repressor (Escherichia coli) (2wrp.R: 2wrp.R) {crossed alpha} [wrp] XXX twisted up down #1tro 1.9 dimer + dsDNA (a2 + d2 + 2 TRP) - 12 chains given [19, 108, 1]; 572 HOHs #1wrp 2.2 dimer (a2) + substrate TRP - 2 chains given [107, 1]; 59 HOHs #2wrp 1.65 dimer (a2) + substrate TRP - 2 chains given [107, 1]; 1 Na+, 1 SO4, and 85 HOHs #3wrp 1.8 dimer (a2) - 1 chain given [108]; apo; 84 HOHs Tryptophan Synthase (Salmonella typhimurium, strain TB2211/PSTH8) (1wsy.A: 1wsy.A) {a/b singly wound para beta + wedge alpha + alpha cap} [barrel] (1wsy.B: 1wsy.B) {domain 1: 9-55,86-206: a/b/a doubly wound para beta ud/ud + crossed alpha + wedge alpha} {domain 2: 56-85,207-393: a/b/a doubly wound para beta ud/cr + crossed alpha + anti beta + alpha} #1wsy 2.5 tetramer (a2b2) - 2 chains given [268, 397]; 1 PLP Tumor Necrosis Factor Alpha (Homo sapiens) (1tnf.A: 1tnf.A) {double stranded beta cylinder} [tnf] XXX Thornton Jelly Roll or {double stranded beta cylinder} #1tnf 2.6 hexamer? (2a3) - 3 chains given [157]; 3 SSs #2tun 3.1 hexamer (2a3) - 6 chains given [157]; A84V mutant; 6 SSs TUS Proline Repeat (Escherichia coli) {proline helix} #1sut NMR fragment - 10 models given [22] ABL Proto-Oncogene Tyrosine Kinase (Homo sapiens) {up down anti beta} #1abl --- monomer? [57]; model, taken from 1shf and 1shg FYN Proto-Oncogene Tyrosine Kinase (Homo sapiens) (1shf.A: 1shf.A [1shg] [1hsp]) {greek + loop anti beta} greek 2.5 loop XXX reverse S + anti beta? #1shf 1.9 fragment - 2 chains given [59]; SH3 domain Proto-Oncogene Tyrosine Kinase (Homo sapiens) (1ab2: 1ab2 [1sha.A]) {a/b/a doubly wound anti beta ud/ud} #1ab2 NMR monomer? - 20 models given [109]; Abelson, C-ABL Tyrosine Phosphatase (Bos Taurus) {a/b/a doubly wound para beta ud/ud} #1bvh NMR monomer - 15 models given [157] Tyrosine Phosphatase SYP (Mus musculus) {a/b/abc doubly wound anti beta ud/ud + anti beta} #1aya 2.05 monomer + peptide - 4 chains given [101, 11]; N-terminal SH2 domain; peptide is PDGFR-1009; 2 PHSs and 141 HOHs #1ayb 3.0 monomer + peptide - 2 chains given [101, 12]; N-terminal SH2 domain; peptide is IRS-1-895; 1 PHS #1ayc 2.3 monomer + peptide - 2 chains given [101, 12]; N-terminal SH2 domain; peptide is PDGFR-740; 1 PHS and 63 HOHs #1ayd 2.2 monomer [101]; N-terminal SH2 domain; 87 HOHs V-SRC Tyrosine Kinase Transforming Protein (Rous Sarcoma Virus) (1sha.A: 1sha.A [1ab2]) {a/b/a doubly wound anti beta ud/ud} #1sha 1.5 fragment + peptide - 2 chains given [104, 5]; phosphotyrosine recognition domain SH2; 1 phosphate on phosphopeptide A and 58 HOHs #1shb 2.0 fragment + peptide - 2 chains given [104, 5]; phosphotyrosine recognition domain SH2; 1 phosphate on phosphopeptide B and 28 HOHs Tyrosine Phenol-Lyase (Citrobacter intermedius) (1tpl.A: 1tpl.A) {domain 1: 1-49+312-456: a/b/a doubly wound para beta} XXX relook {domain 2: 50-311: a/b open face anti beta + anti beta + alpha} #1tpl 2.3 tetramer (a4) - 2 chains given [426]; SEQRES records list 426 residues, but ATOM records are numbered through residue 456; 4 SO4s and 450 HOHs Tyrosyl-tRNA Synthetase (Bacillus stearothermophilus) (2ts1: 2ts1) {domain 1: 1-222: a/b/a doubly wound para beta ud/ud + wedge alpha + alpha} {domain 2: 223-319: double stranded alpha cylinder} [2ts1] #2ts1 2.3 dimer (a2) - 1 chain given [419]; supersedes 1ts1; 110 HOHs #3ts1 2.7 dimer (a2) - 1 chain given [419]; 1 tyrosinyl adenylate and 54 HOHs #4ts1 2.5 dimer (a2) + substrate - 4 chains given [319, 1]; DEL(318-417) mutant; 144 HOHs #1tya 2.8 dimer (a2) + substrate - 2 chains given [319, 1]; T51A mutant; 162 HOHs #1tyb 2.5 dimer (a2) + substrate - 2 chains given [319, 1]; T51G mutant; 165 HOHs #1tyc 2.5 dimer (a2) - 1 chain given [319]; T51P mutant; 171 HOHs #1tyd 2.5 dimer (a2) + substrate - 2 chains given [319, 1]; T51S mutant; 163 HOHs U1 Small Nuclear Ribonuclear Protein (Homo sapiens) (1nrc.A: 1nrc.A) {a/b open face anti beta cr} #1nrc 2.8 CA monomer - 2 chains given [95]; N-terminal fragment; Q85C mutant Ubiquitin (Bos taurus and Homo sapiens) (1ubq: 1ubq) {a/b open face anti beta cr} [fxc] XXX Thornton twisted beta 2 #1aar 2.3 dimer (a2) - 2 chains given [76]; di-ubiquitin; 15 HOHs; Bos taurus #1tbe 2.4 tetramer (a4) - 2 chains given; tetraubiquitin; Homo sapiens #1ubq 1.8 monomer [76]; 58 HOHs; Homo sapiens Ubiquitin Conjugating Enzyme E2 (Arabidopsis thaliana) (1aak: 1aak [2uce]) {domain 1: 1-123: a/b open face anti beta cr + alpha} {domain 2: 124-151: wedge alpha} #1aak 2.4 monomer? [152]; 6 HOHs Ubiquitin Conjugating Enzyme (Saccharomyces cerevisiae) (2uce: 2uce [1aak]) {domain 1: 1-121: a/b open face anti beta cr + alpha} {domain 2: 122-148: wedge alpha} #2uce 2.7 monomer? [148] Uridine Diphosphogalactose 4-Epimerase (Escherichia coli) (1udp.A: 1udp.A) {domain 1: 1-181,236-261: a/b/a doubly wound para beta ud/ud} {domain 2: 182-235,262-338: schief para 3-helix bundle + anti beta} #1udp 2.5 CA dimer? (a2) - 2 chains given [338] Uteroglobin (Oryctolagus cuniculus) (1utg: 1utg) {up down anti alpha} [utg] XXX twisted up down #1utg 1.34 dimer (a2) - 1 chain given [70]; oxidized; 83 HOHs #2utg 1.64 dimer (a2) - 2 chains given [70]; 165 HOHs; 2 SSs Vancomycin (Streptomyces sp.) (1van.P: ***) {coil} #1van --- peptide [3]; 1 vancomycin; non-experimental model Variant Surface Glycoprotein (Trypanosoma brucei) (1vsg.A: 1vsg.A) {up down anti alpha + anti beta + crossed alpha} XXX look again #1vsg 2.9 dimer (a2) - 2 chains given [364]; 4 NAGs, 2 MANs, and 18 HOHs; 4 SSs Vesicular Stomatitis Virus Nucleoprotein (VSV-8) (1vaa.P: 1vaa.P) {coil} DUP1vaa 2.3 fragment + microglobulin + MHC - 3 chains given [8, 99, 274]; 114 HOHs; 3 SSs Verotoxin-I (Escherichia coli) (1bov.A: 1bov.A) {greek + loop anti beta + alpha cap} see 1chb reverse S + anti beta loop #1bov 2.2 pentamer? (a5) - 5 chains given [69]; oligomer; 3 Zns and 98 HOHs; 5 SSs Vigilin (Homo sapiens) {a/b open face anti beta} #1vig NMR fragment - 40 models given [71] Villin (Gallus gallus) (1vil: 1vil) {a/b/a doubly wound mixed beta ud/cr + para beta} #1vil NMR fragment - 10 models given [126]; N-terminal domain Wheat Germ Agglutinin, Isolectin 1 (Triticum vulgaris) Isolectins 1 and 2 differ by 5 residues. (7wga.A: 9wga.A [1hev]) {domain 1: 1-42: SS rich a/b/c doubly wound anti beta cr/ud} [wga] {domain 2: 43-84: SS rich a/b/a doubly wound anti beta cr/cr} [wga] {domain 3: 85-128: SS rich a/b/c doubly wound anti beta cr/ud} [wga] {domain 4: 129-171: SS rich a/b/c doubly wound anti beta cr/ud} [wga] #2cwg 2.0 dimer (a2) + peptide (2p) - 4 chains given [171, 8]; isolectin 1; T5 sialoglycopeptide of glycophorin A; 4 sialic acids, 2 GALs, 2 NGAs, and 389 HOHs; 32 SSs #7wga 2.0 dimer (a2) - 2 chains given [171]; isolectin 1; 217 HOHs; 32 SSs #1wgc 2.2 dimer (a2) - 2 chains given [171]; isolectin 1; 2 sialic acids, 2 GALs, 2 GLCs, and 217 HOHs; 32 SSs Wheat Germ Agglutinin, Isolectin 2 (Triticum vulgaris) Isolectins 1 and 2 differ by 5 residues. (9wga.A: 9wga.A [1hev]) {domain 1: 1-42: SS rich a/b/a doubly wound anti beta cr/cr} [wga] {domain 2: 43-84: SS rich a/b/c doubly wound anti beta cr/ud} [wga] {domain 3: 85-128: SS rich a/b/c doubly wound anti beta cr/ud} [wga] {domain 4: 129-171: SS rich a/b/c doubly wound anti beta cr/ud} [wga] #9wga 1.8 dimer (a2) - 2 chains given [171]; supersedes 3wga; isolectin 2; 231 HOHs; 32 SSs #2wgc 2.2 dimer (a2) - 2 chains given [171]; isolectin 2; 2 sialic acids, 2 GALs, 2 GLCs, and 235 HOHs; 32 SSs Xylanase (Bacillus Circulans) {Greek anti beta + alpha} XXX multiple Greek folded over #1bcx 1.8 monomer? [185]; 1 SO4, 2 XYSs, and 144 HOHs Xylose Isomerase (Actinoplanes missouriensis) (1xim.A: 1xis) {domain 1: 1-329: a/b singly wound para beta} {domain 2: 330-396: up down anti alpha + coil + alpha} [xia+] #1xim 2.2 tetramer (a4) - 4 chains given [393]; 8 Co++s, 4 XYLs, and 881 HOHs #2xim 2.3 tetramer (a4) - 4 chains given [393]; K253R mutant; 8 Mg++s, 4 XLSs, and 919 HOHs #3xim 2.3 tetramer (a4) - 4 chains given [393]; K309R, K319R, K323R mutant; 8 Co++s, 4 SORs, and 871 HOHs #4xim 2.3 tetramer (a4) - 4 chains given [393]; 8 Co++s and 837 HOHs #5xim 2.6 tetramer (a4) - 4 chains given [393]; 4 Mg++s, 4 SORs, and 868 HOHs #6xim 2.5 tetramer (a4) - 4 chains given [393]; 8 Mg++s, 4 XLSs, and 881 HOHs #7xim 2.4 tetramer (a4) - 4 chains given [393]; demetallized, pH 5, EDTA; 895 HOHs #8xim 2.4 tetramer (a4) - 4 chains given [393]; E186Q mutant; 4 Mg++s, 4 XLSs, and 971 HOHs #9xim 2.4 tetramer (a4) - 4 chains given [393]; E186Q mutant; 4 Mn++s, 4 XLSs, and 978 HOHs #1xin 2.4 tetramer (a4) - 4 chains given [393]; H220N mutant; 4 Mg++s, 4 XLSs, and 889 HOHs #2xin 2.3 tetramer (a4) - 4 chains given [393]; H290N mutant; 8 Co++s, 4 SORs, and 900 HOHs #3xin 2.3 tetramer (a4) - 4 chains given [393]; E181Q mutant; 904 HOHs #5xin 2.3 tetramer (a4) - 4 chains given [393]; D255A mutant; 4 Mg++s, 4 XLSs, and 881 HOHs Xylose Isomerase (Arthrobacter strain B3728) (4xia.A: 1xis) {domain 1: 1-328: a/b singly wound para beta} {domain 2: 329-399: up down anti alpha + coil + alpha} [xia] #1did 2.5 tetramer (a4) - 2 chains given [394]; 4 Mn++s, 2 2,5-dideoxy- 2,5-imino-D-glucitols, and 504 HOHs #1die 2.5 tetramer (a4) - 2 chains given [394]; 4 Mn++s, 2 2,5-dideoxy- 2,5-nojirimycin, and HOHs #1xia 2.3 CA tetramer (a4) - 2 chains given [393]; all residues UNK #4xia 2.3 tetramer (a4) - 2 chains given [393]; 2 SORs, 2 Mg++s, and 538 HOHs #5xia 2.5 tetramer (a4) - 2 chains given [393]; 2 XYLs, 2 Mg++s, and 575 HOHs #1xla 2.3 tetramer (a4) - 2 chains given [394]; apo form; 579 HOHs #1xlb 2.5 tetramer (a4) - 2 chains given [394]; 2 Mg++s and 586 HOHs #1xlc 2.5 tetramer (a4) - 2 chains given [394]; 2 XLSs, 2 Mg++s, and 536 HOHs #1xld 2.5 tetramer (a4) - 2 chains given [394]; 2 XLSs, 4 Mn++s, and 500 HOHs #1xle 2.5 tetramer (a4) - 2 chains given [394]; 4 Mn++s and 522 HOHs #1xlf 2.5 tetramer (a4) - 2 chains given [394]; 2 gluconates, 4 Mn++s, and 515 HOHs #1xlg 2.5 tetramer (a4) - 2 chains given [394]; 2 XLSs, 2 Mg++s, 2 Al++s, and 536 HOHs #1xlh 2.5 tetramer (a4) - 2 chains given [394]; 2 Al++s and 546 HOHs #1xli 2.5 tetramer (a4) - 2 chains given [394]; 2 5-thio-alpha-D-glucoses, 4 Mn++s, and 519 HOHs #1xlj 2.5 tetramer (a4) - 2 chains given [394]; 2 XYLs, 2 Mn++s, and 514 HOHs #1xlk 2.5 tetramer (a4) - 2 chains given [394]; 4 Mn++s and 522 HOHs #1xll 2.5 tetramer (a4) - 2 chains given [394]; 4 Zn++s and 525 HOHs Xylose Isomerase (Streptomyces albus) (6xia: 1xis) {domain 1: 1-322: a/b singly wound para beta} {domain 2: 323-387: up down anti alpha + coil + alpha} [xia+] #6xia 1.65 tetramer (a4) - 1 chain given [387]; 454 HOHs Xylose Isomerase (Streptomyces murinus) (1dxi.A: 1xis) {domain 1: 1-323: a/b singly wound para beta} {domain 2: 324-388: up down anti alpha + coil + alpha} [xia+] #1dxi 2.6 tetramer (a4) - 2 chains given [388]; 4 Mg++s and 4 HOHs Xylose Isomerase (Streptomyces rubiginosus) (1xis: 1xis) {domain 1: 2-323: a/b singly wound para beta} {domain 2: 324-388: up down anti alpha + coil + alpha} [xia+] #7xia 1.9 tetramer (a4) - 1 chain given [388]; supersedes 2xia; 2 Mns and 306 HOHs #8xia 1.9 tetramer (a4) - 1 chain given [388]; 1 XLS, 2 Mns, and 291 HOHs #9xia 1.9 tetramer (a4) - 1 chain given [388]; 1 3-deoxy-C3-methylene- D-fructose, 2 Mns, and 299 HOHs #1xis 1.60 tetramer (a4) - 1 chain given [387]; 2 Mn++s and 407 HOHs #2xis 1.71 tetramer (a4) - 1 chain given [387]; 1 XYL, 2 Mgs and 345 HOHs #3xis 1.60 tetramer (a4) - 1 chain given [387]; 1 XLS, 1 cyclic xylose, 2 Mgs and 362 HOHs #4xis 1.60 tetramer (a4) - 1 chain given [387]; 1 XLS, 1 cyclic xylose, 2 Mns and 404 HOHs ZFY-6T Zinc Finger (Homo sapiens) (5znf: 5znf) {metal rich a/b open face anti beta} [finger+] #5znf NMR monomer - 13 models given [30]; 2 aas diff from 7znf; 1 Zn++ ZFY-Swap Zinc Finger (Homo sapiens) (7znf: 5znf) {metal rich a/b open face anti beta} [finger+] #7znf NMR monomer - 12 models given [30]; 2 aas diff from 5znf; 1 Zn++ ZIF268 Immediate Early Gene (Homo sapiens) (1zaa.C: 1zaa.C [1ard] [1znf]) {domain 1: 3-33: metal rich a/b open face anti beta} [finger+] {domain 2: 34-60: metal rich a/b open face anti beta} [finger+] {domain 3: 61-87: metal rich a/b open face anti beta} [finger+] #1zaa 2.1 monomer + dsDNA - 3 chains given [85, 11]; 3 Zn++s and 129 HOHs Zinc Finger (Homo sapiens) (3znf: 1zaa.C [1znf] [1ard]) {metal rich a/b open face anti beta} [finger+] #3znf NMR monomer [30]; minimized average structure; 1 Zn #4znf NMR monomer - 41 models given [30]; 1 Zn Zinc Finger (Xenopus lavis) (1znf: 1znf [1zaa.C] [1ard]) {metal rich a/b open face anti beta} [finger+] #1znf NMR monomer - 37 models given [27]; 31st zinc finger from XFIN; model 1 to be used for geometry; 1 Zn and 1 terminal amide