HEADER HYDROLASE/HYDROLASE INHIBITOR 20-JUL-11 3B23 TITLE CRYSTAL STRUCTURE OF THROMBIN-VARIEGIN COMPLEX: INSIGHTS OF A NOVEL TITLE 2 MECHANISM OF INHIBITION AND DESIGN OF TUNABLE THROMBIN INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-THROMBIN, LIGHT CHAIN; COMPND 5 EC: 3.4.21.5; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: ALPHA-THROMBIN, HEAVY CHAIN; COMPND 11 EC: 3.4.21.5; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: VARIEGIN; COMPND 15 CHAIN: C; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F2; SOURCE 6 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SP2/0 AG14 MOUSE MYELOMA CELLS (ATCC SOURCE 10 CRL-1581); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCAGG/MDHFR/PRETHROMBIN-2; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: F2; SOURCE 18 EXPRESSION_SYSTEM: MUS MUSCULUS; SOURCE 19 EXPRESSION_SYSTEM_COMMON: MOUSE; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 10090; SOURCE 21 EXPRESSION_SYSTEM_CELL_LINE: SP2/0 AG14 MOUSE MYELOMA CELLS (ATCC SOURCE 22 CRL-1581); SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PCAGG/MDHFR/PRETHROMBIN-2; SOURCE 25 MOL_ID: 3; SOURCE 26 SYNTHETIC: YES; SOURCE 27 ORGANISM_SCIENTIFIC: AMBLYOMMA VARIEGATUM; SOURCE 28 ORGANISM_COMMON: TROPICAL BONT TICK; SOURCE 29 ORGANISM_TAXID: 34610; SOURCE 30 OTHER_DETAILS: PEPTIDE IS CHEMICALLY SYNTHESIZED BASED ON SEQUENCE SOURCE 31 OF A THROMBIN INHIBITOR FOUND IN THE SALIVARY GLAND EXTRACT OF SOURCE 32 AMBLYOMMA VARIEGATUM KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.KOH,S.KUMAR,K.SWAMINATHAN,R.M.KINI REVDAT 1 23-NOV-11 3B23 0 JRNL AUTH C.Y.KOH,S.KUMAR,M.KAZIMIROVA,P.A.NUTTALL,U.P.RADHAKRISHNAN, JRNL AUTH 2 S.KIM,P.JAGADEESWARAN,T.IMAMURA,J.MIZUGUCHI,S.IWANAGA, JRNL AUTH 3 K.SWAMINATHAN,R.M.KINI JRNL TITL CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH S-VARIEGIN: JRNL TITL 2 INSIGHTS OF A NOVEL MECHANISM OF INHIBITION AND DESIGN OF JRNL TITL 3 TUNABLE THROMBIN INHIBITORS JRNL REF PLOS ONE V. 6 26367 2011 JRNL REFN ESSN 1932-6203 JRNL PMID 22053189 JRNL DOI 10.1371/JOURNAL.PONE.0026367 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 13298 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 724 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 659 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2464 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 51 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.05000 REMARK 3 B22 (A**2) : 2.49000 REMARK 3 B33 (A**2) : -2.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.79000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.208 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.862 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2534 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1793 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3427 ; 1.224 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4343 ; 0.811 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 6.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 121 ;32.426 ;23.471 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 444 ;14.327 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.229 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 355 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2786 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 529 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1516 ; 0.490 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 613 ; 0.078 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2447 ; 0.931 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1018 ; 1.191 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 980 ; 1.936 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 14 REMARK 3 ORIGIN FOR THE GROUP (A): 4.0794 -16.8468 8.3862 REMARK 3 T TENSOR REMARK 3 T11: 0.2998 T22: 0.1748 REMARK 3 T33: 0.2081 T12: -0.1234 REMARK 3 T13: -0.1240 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 7.7683 L22: 7.5350 REMARK 3 L33: 7.2261 L12: -5.3954 REMARK 3 L13: 4.3074 L23: -4.2133 REMARK 3 S TENSOR REMARK 3 S11: 0.6151 S12: 0.1421 S13: -0.4183 REMARK 3 S21: -0.3334 S22: -0.2657 S23: 0.5826 REMARK 3 S31: 0.9106 S32: -0.3790 S33: -0.3494 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 16 B 247 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3728 -8.3738 14.5645 REMARK 3 T TENSOR REMARK 3 T11: 0.0587 T22: 0.1884 REMARK 3 T33: 0.0558 T12: -0.0290 REMARK 3 T13: -0.0150 T23: 0.0446 REMARK 3 L TENSOR REMARK 3 L11: 3.0952 L22: 2.2568 REMARK 3 L33: 4.9670 L12: -0.1513 REMARK 3 L13: 1.9526 L23: -0.4062 REMARK 3 S TENSOR REMARK 3 S11: 0.1532 S12: 0.3764 S13: 0.1639 REMARK 3 S21: 0.1246 S22: -0.2425 S23: -0.1438 REMARK 3 S31: 0.0703 S32: 0.8190 S33: 0.0892 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3B23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-AUG-11. REMARK 100 THE RCSB ID CODE IS RCSB029981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15137 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.15400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1ABI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES BUFFER PH 7.4, 20-25% (W/ REMARK 280 V) PEG 8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 62.32900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.41300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.32900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.41300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 1H REMARK 465 PHE A 1G REMARK 465 GLY A 1F REMARK 465 SER A 1E REMARK 465 GLY A 1D REMARK 465 GLU A 1C REMARK 465 ARG A 15 REMARK 465 SER C 1 REMARK 465 ASP C 2 REMARK 465 GLN C 3 REMARK 465 GLY C 4 REMARK 465 ASP C 5 REMARK 465 VAL C 6 REMARK 465 ALA C 7 REMARK 465 GLU C 8 REMARK 465 PRO C 9 REMARK 465 LYS C 10 REMARK 465 MET C 11 REMARK 465 ASP C 29 REMARK 465 ASP C 30 REMARK 465 GLU C 31 REMARK 465 SER C 32 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 145 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 7 O LYS A 10 2.07 REMARK 500 O HOH B 261 O HOH B 270 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 7 -75.04 -133.30 REMARK 500 TYR B 60A 80.60 -158.44 REMARK 500 ASN B 60G 80.88 -156.69 REMARK 500 HIS B 71 -53.26 -122.73 REMARK 500 ILE B 79 -54.75 -132.78 REMARK 500 ASN B 95 75.31 -103.23 REMARK 500 GLU B 97A -59.09 -135.62 REMARK 500 ASN B 98 18.36 -147.43 REMARK 500 ALA B 149A -111.89 68.96 REMARK 500 LYS B 149E 46.17 -72.87 REMARK 500 ALA C 15 149.39 -179.46 REMARK 500 GLU C 25 79.56 -108.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF VARIEGIN DBREF 3B23 A 1H 15 UNP P00734 THRB_HUMAN 328 363 DBREF 3B23 B 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 3B23 C 1 32 UNP P85800 VARI_AMBVA 1 32 SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 C 32 SER ASP GLN GLY ASP VAL ALA GLU PRO LYS MET HIS LYS SEQRES 2 C 32 THR ALA PRO PRO PHE ASP PHE GLU ALA ILE PRO GLU GLU SEQRES 3 C 32 TYR LEU ASP ASP GLU SER FORMUL 4 HOH *51(H2 O) HELIX 1 1 THR A 14B ASP A 14L 1 11 HELIX 2 2 ALA B 55 CYS B 58 5 4 HELIX 3 3 PRO B 60B ASP B 60E 5 4 HELIX 4 4 THR B 60I ASN B 62 5 3 HELIX 5 5 ASP B 125 LEU B 130 1 9 HELIX 6 6 VAL B 149C GLN B 151 5 5 HELIX 7 7 GLU B 164 SER B 171 1 8 HELIX 8 8 LYS B 185 GLY B 186C 5 5 HELIX 9 9 LEU B 234 GLY B 246 1 13 SHEET 1 A 7 SER B 20 ASP B 21 0 SHEET 2 A 7 GLN B 156 PRO B 161 -1 O VAL B 157 N SER B 20 SHEET 3 A 7 LYS B 135 GLY B 140 -1 N VAL B 138 O VAL B 158 SHEET 4 A 7 PRO B 198 LYS B 202 -1 O VAL B 200 N ARG B 137 SHEET 5 A 7 TRP B 207 TRP B 215 -1 O TYR B 208 N MET B 201 SHEET 6 A 7 GLY B 226 HIS B 230 -1 O THR B 229 N ILE B 212 SHEET 7 A 7 MET B 180 ALA B 183 -1 N PHE B 181 O TYR B 228 SHEET 1 B 7 LYS B 81 SER B 83 0 SHEET 2 B 7 LEU B 64 ILE B 68 -1 N VAL B 66 O SER B 83 SHEET 3 B 7 GLN B 30 ARG B 35 -1 N MET B 32 O ARG B 67 SHEET 4 B 7 GLU B 39 LEU B 46 -1 O GLU B 39 N ARG B 35 SHEET 5 B 7 TRP B 51 THR B 54 -1 O LEU B 53 N SER B 45 SHEET 6 B 7 ALA B 104 LEU B 108 -1 O ALA B 104 N THR B 54 SHEET 7 B 7 LEU B 85 ILE B 90 -1 N GLU B 86 O LYS B 107 SHEET 1 C 2 LEU B 60 TYR B 60A 0 SHEET 2 C 2 LYS B 60F ASN B 60G-1 O LYS B 60F N TYR B 60A SSBOND 1 CYS A 1 CYS B 122 1555 1555 2.07 SSBOND 2 CYS B 42 CYS B 58 1555 1555 2.05 SSBOND 3 CYS B 168 CYS B 182 1555 1555 2.05 SSBOND 4 CYS B 191 CYS B 220 1555 1555 2.09 CISPEP 1 SER B 36A PRO B 37 0 -4.37 SITE 1 AC1 30 PHE B 34 GLN B 38 GLU B 39 LEU B 40 SITE 2 AC1 30 LEU B 41 TYR B 60A TRP B 60D LYS B 60F SITE 3 AC1 30 LEU B 65 ARG B 67 ARG B 73 THR B 74 SITE 4 AC1 30 ARG B 75 TYR B 76 ARG B 77A ASN B 143 SITE 5 AC1 30 THR B 147 TRP B 148 VAL B 149C GLN B 151 SITE 6 AC1 30 ARG B 173 ILE B 174 GLU B 192 SER B 195 SITE 7 AC1 30 HOH B 266 HOH C 33 HOH C 34 HOH C 49 SITE 8 AC1 30 HOH C 50 HOH C 278 CRYST1 124.658 50.826 61.535 90.00 98.70 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008022 0.000000 0.001228 0.00000 SCALE2 0.000000 0.019675 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016440 0.00000