HEADER HYDROLASE 16-JUL-17 5WHC TITLE USP7 IN COMPLEX WITH CPD2 (4-(3-(1-METHYLPIPERIDIN-4-YL)-1,2,4- TITLE 2 OXADIAZOL-5-YL)PHENOL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 209-554; COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 6 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- COMPND 7 PROCESSING PROTEASE 7; COMPND 8 EC: 3.4.19.12; COMPND 9 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: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HAUSP, SBDD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.MURRAY,L.ROUGE REVDAT 3 04-OCT-23 5WHC 1 REMARK REVDAT 2 10-JAN-18 5WHC 1 JRNL REVDAT 1 13-DEC-17 5WHC 0 JRNL AUTH P.DI LELLO,R.PASTOR,J.M.MURRAY,R.A.BLAKE,F.COHEN, JRNL AUTH 2 T.D.CRAWFORD,J.DROBNICK,J.DRUMMOND,L.KATEGAYA,T.KLEINHEINZ, JRNL AUTH 3 T.MAURER,L.ROUGE,X.ZHAO,I.WERTZ,C.NDUBAKU,V.TSUI JRNL TITL DISCOVERY OF SMALL-MOLECULE INHIBITORS OF UBIQUITIN SPECIFIC JRNL TITL 2 PROTEASE 7 (USP7) USING INTEGRATED NMR AND IN SILICO JRNL TITL 3 TECHNIQUES. JRNL REF J. MED. CHEM. V. 60 10056 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 29166018 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01293 REMARK 2 REMARK 2 RESOLUTION. 2.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2747) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 25586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1310 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 76.8111 - 5.2998 0.96 2767 128 0.1879 0.2507 REMARK 3 2 5.2998 - 4.2067 0.97 2716 155 0.1682 0.2035 REMARK 3 3 4.2067 - 3.6749 0.97 2702 129 0.1932 0.2249 REMARK 3 4 3.6749 - 3.3389 0.95 2647 145 0.2194 0.2782 REMARK 3 5 3.3389 - 3.0996 0.98 2732 144 0.2569 0.3219 REMARK 3 6 3.0996 - 2.9169 0.98 2709 160 0.2462 0.3202 REMARK 3 7 2.9169 - 2.7708 0.95 2610 148 0.2781 0.3206 REMARK 3 8 2.7708 - 2.6502 0.97 2664 162 0.2843 0.3364 REMARK 3 9 2.6502 - 2.5481 0.98 2729 139 0.3223 0.3790 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 5622 REMARK 3 ANGLE : 0.534 7580 REMARK 3 CHIRALITY : 0.041 810 REMARK 3 PLANARITY : 0.003 1012 REMARK 3 DIHEDRAL : 16.183 3422 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 209 THROUGH 325 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.6516 6.6000 -0.4106 REMARK 3 T TENSOR REMARK 3 T11: 0.7545 T22: 0.6249 REMARK 3 T33: 0.6224 T12: -0.1121 REMARK 3 T13: 0.0538 T23: -0.1239 REMARK 3 L TENSOR REMARK 3 L11: 3.4912 L22: 2.3517 REMARK 3 L33: 3.3906 L12: 1.0288 REMARK 3 L13: 0.2999 L23: 0.0364 REMARK 3 S TENSOR REMARK 3 S11: 0.1058 S12: -0.1537 S13: -0.4559 REMARK 3 S21: 0.5127 S22: -0.3300 S23: 0.2557 REMARK 3 S31: 0.4479 S32: -0.1939 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 326 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.1776 17.2241 -0.1994 REMARK 3 T TENSOR REMARK 3 T11: 0.6562 T22: 0.6149 REMARK 3 T33: 0.7359 T12: -0.0860 REMARK 3 T13: -0.1130 T23: 0.0393 REMARK 3 L TENSOR REMARK 3 L11: 4.6601 L22: 2.4836 REMARK 3 L33: 0.5065 L12: -1.2666 REMARK 3 L13: -0.4416 L23: 0.3140 REMARK 3 S TENSOR REMARK 3 S11: -0.0165 S12: -0.1678 S13: 0.1766 REMARK 3 S21: 0.4273 S22: -0.1146 S23: -0.7036 REMARK 3 S31: 0.1052 S32: 0.1029 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 554 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.1948 18.0342 -1.2053 REMARK 3 T TENSOR REMARK 3 T11: 0.5704 T22: 0.6892 REMARK 3 T33: 0.6300 T12: -0.0400 REMARK 3 T13: 0.0424 T23: -0.1243 REMARK 3 L TENSOR REMARK 3 L11: 3.6694 L22: 5.1064 REMARK 3 L33: 1.0534 L12: 1.0401 REMARK 3 L13: -0.1750 L23: 0.1034 REMARK 3 S TENSOR REMARK 3 S11: 0.3025 S12: -0.1801 S13: 0.2553 REMARK 3 S21: 0.4549 S22: -0.5230 S23: 0.6848 REMARK 3 S31: 0.1593 S32: -0.3109 S33: -0.0012 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 209 THROUGH 325 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.2415 4.2739 37.8256 REMARK 3 T TENSOR REMARK 3 T11: 0.7594 T22: 0.6466 REMARK 3 T33: 0.7296 T12: -0.0105 REMARK 3 T13: 0.1168 T23: -0.1127 REMARK 3 L TENSOR REMARK 3 L11: 2.6592 L22: 3.7103 REMARK 3 L33: 3.1404 L12: -0.8155 REMARK 3 L13: -0.2531 L23: -0.2196 REMARK 3 S TENSOR REMARK 3 S11: -0.3370 S12: 0.2771 S13: -0.3561 REMARK 3 S21: -0.4537 S22: 0.2516 S23: -0.5081 REMARK 3 S31: 0.3125 S32: -0.0366 S33: 0.0000 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 326 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4339 14.9857 38.7643 REMARK 3 T TENSOR REMARK 3 T11: 0.7006 T22: 0.7150 REMARK 3 T33: 0.6808 T12: 0.0212 REMARK 3 T13: -0.0589 T23: 0.0526 REMARK 3 L TENSOR REMARK 3 L11: 3.9145 L22: 3.1266 REMARK 3 L33: -0.0813 L12: 1.7541 REMARK 3 L13: 0.6349 L23: 0.6949 REMARK 3 S TENSOR REMARK 3 S11: -0.2835 S12: 0.2112 S13: 0.0685 REMARK 3 S21: -0.3233 S22: 0.1973 S23: 0.5801 REMARK 3 S31: 0.0470 S32: -0.1245 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 460 THROUGH 554 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.7004 15.7867 39.1487 REMARK 3 T TENSOR REMARK 3 T11: 0.6804 T22: 0.7017 REMARK 3 T33: 0.6394 T12: -0.0328 REMARK 3 T13: 0.0522 T23: -0.1076 REMARK 3 L TENSOR REMARK 3 L11: 3.8500 L22: 4.2650 REMARK 3 L33: 0.9346 L12: -0.3147 REMARK 3 L13: -0.0607 L23: -0.1715 REMARK 3 S TENSOR REMARK 3 S11: -0.2043 S12: 0.1581 S13: 0.1461 REMARK 3 S21: -0.4929 S22: 0.1491 S23: -0.7031 REMARK 3 S31: 0.0919 S32: 0.1752 S33: -0.0003 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5WHC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1000229024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25643 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.548 REMARK 200 RESOLUTION RANGE LOW (A) : 76.776 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL 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) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1NB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, 0.1M TRIS-HCL 7.0, PH 7.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.63950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 HIS A 501 REMARK 465 ASP A 502 REMARK 465 ASP A 503 REMARK 465 ASP A 504 REMARK 465 LEU A 505 REMARK 465 SER A 506 REMARK 465 VAL A 507 REMARK 465 ARG A 508 REMARK 465 HIS B 501 REMARK 465 ASP B 502 REMARK 465 ASP B 503 REMARK 465 ASP B 504 REMARK 465 LEU B 505 REMARK 465 SER B 506 REMARK 465 VAL B 507 REMARK 465 ARG B 508 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 TYR A 411 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 412 CG OD1 OD2 REMARK 470 GLN A 414 CG CD OE1 NE2 REMARK 470 THR A 415 OG1 CG2 REMARK 470 ASP A 416 CG OD1 OD2 REMARK 470 GLN A 417 CG CD OE1 NE2 REMARK 470 TYR B 411 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP B 412 CG OD1 OD2 REMARK 470 GLN B 414 CG CD OE1 NE2 REMARK 470 THR B 415 OG1 CG2 REMARK 470 ASP B 416 CG OD1 OD2 REMARK 470 GLN B 417 CG CD OE1 NE2 REMARK 470 ASN B 418 CG OD1 ND2 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLN B 414 REMARK 475 THR B 415 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 HOH A 715 O HOH A 719 1.82 REMARK 500 N GLY B 356 O HOH B 701 2.15 REMARK 500 OD2 ASP B 459 ND1 HIS B 461 2.16 REMARK 500 OH TYR B 367 O HOH B 702 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN B 309 CA - C - O ANGL. DEV. = 13.6 DEGREES REMARK 500 PRO B 413 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 PRO B 413 C - N - CD ANGL. DEV. = -15.8 DEGREES 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 ALA A 221 43.68 -68.12 REMARK 500 CYS A 223 -121.81 60.79 REMARK 500 PRO A 246 91.40 -69.70 REMARK 500 SER A 252 10.01 -64.99 REMARK 500 ASN A 377 40.10 -88.22 REMARK 500 ASP A 416 -54.25 -138.51 REMARK 500 ASP A 459 -155.81 -91.21 REMARK 500 PHE A 480 78.65 -104.83 REMARK 500 ASP A 482 -122.50 55.39 REMARK 500 ILE A 494 -71.58 -108.06 REMARK 500 HIS B 210 23.47 -74.65 REMARK 500 ALA B 221 52.14 -94.00 REMARK 500 CYS B 223 -124.50 61.62 REMARK 500 PRO B 246 85.78 -68.55 REMARK 500 SER B 252 5.57 -66.66 REMARK 500 TRP B 285 69.04 -114.64 REMARK 500 ASN B 377 51.21 -115.93 REMARK 500 ALA B 381 31.00 -94.28 REMARK 500 ASP B 416 15.79 135.86 REMARK 500 ILE B 419 -178.10 -65.84 REMARK 500 PHE B 480 78.72 -112.80 REMARK 500 ASP B 482 -123.07 55.29 REMARK 500 ILE B 494 -73.26 -112.92 REMARK 500 HIS B 534 12.89 -68.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 414 THR A 415 -141.38 REMARK 500 PRO B 413 GLN B 414 -32.68 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 residue AJJ A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AJJ B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WH7 RELATED DB: PDB DBREF 5WHC A 209 554 UNP Q93009 UBP7_HUMAN 209 554 DBREF 5WHC B 209 554 UNP Q93009 UBP7_HUMAN 209 554 SEQRES 1 A 346 LYS HIS THR GLY TYR VAL GLY LEU LYS ASN GLN GLY ALA SEQRES 2 A 346 THR CYS TYR MET ASN SER LEU LEU GLN THR LEU PHE PHE SEQRES 3 A 346 THR ASN GLN LEU ARG LYS ALA VAL TYR MET MET PRO THR SEQRES 4 A 346 GLU GLY ASP ASP SER SER LYS SER VAL PRO LEU ALA LEU SEQRES 5 A 346 GLN ARG VAL PHE TYR GLU LEU GLN HIS SER ASP LYS PRO SEQRES 6 A 346 VAL GLY THR LYS LYS LEU THR LYS SER PHE GLY TRP GLU SEQRES 7 A 346 THR LEU ASP SER PHE MET GLN HIS ASP VAL GLN GLU LEU SEQRES 8 A 346 CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN LYS MET LYS SEQRES 9 A 346 GLY THR CYS VAL GLU GLY THR ILE PRO LYS LEU PHE ARG SEQRES 10 A 346 GLY LYS MET VAL SER TYR ILE GLN CYS LYS GLU VAL ASP SEQRES 11 A 346 TYR ARG SER ASP ARG ARG GLU ASP TYR TYR ASP ILE GLN SEQRES 12 A 346 LEU SER ILE LYS GLY LYS LYS ASN ILE PHE GLU SER PHE SEQRES 13 A 346 VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP GLY ASP ASN SEQRES 14 A 346 LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN GLU ALA GLU SEQRES 15 A 346 LYS GLY VAL LYS PHE LEU THR LEU PRO PRO VAL LEU HIS SEQRES 16 A 346 LEU GLN LEU MET ARG PHE MET TYR ASP PRO GLN THR ASP SEQRES 17 A 346 GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU PHE PRO GLU SEQRES 18 A 346 GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS THR ASP PRO SEQRES 19 A 346 LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA VAL LEU VAL SEQRES 20 A 346 HIS SER GLY ASP ASN HIS GLY GLY HIS TYR VAL VAL TYR SEQRES 21 A 346 LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS LYS PHE ASP SEQRES 22 A 346 ASP ASP VAL VAL SER ARG CYS THR LYS GLU GLU ALA ILE SEQRES 23 A 346 GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP LEU SER VAL SEQRES 24 A 346 ARG HIS CYS THR ASN ALA TYR MET LEU VAL TYR ILE ARG SEQRES 25 A 346 GLU SER LYS LEU SER GLU VAL LEU GLN ALA VAL THR ASP SEQRES 26 A 346 HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU SEQRES 27 A 346 GLU LYS ARG ILE GLU ALA GLN LYS SEQRES 1 B 346 LYS HIS THR GLY TYR VAL GLY LEU LYS ASN GLN GLY ALA SEQRES 2 B 346 THR CYS TYR MET ASN SER LEU LEU GLN THR LEU PHE PHE SEQRES 3 B 346 THR ASN GLN LEU ARG LYS ALA VAL TYR MET MET PRO THR SEQRES 4 B 346 GLU GLY ASP ASP SER SER LYS SER VAL PRO LEU ALA LEU SEQRES 5 B 346 GLN ARG VAL PHE TYR GLU LEU GLN HIS SER ASP LYS PRO SEQRES 6 B 346 VAL GLY THR LYS LYS LEU THR LYS SER PHE GLY TRP GLU SEQRES 7 B 346 THR LEU ASP SER PHE MET GLN HIS ASP VAL GLN GLU LEU SEQRES 8 B 346 CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN LYS MET LYS SEQRES 9 B 346 GLY THR CYS VAL GLU GLY THR ILE PRO LYS LEU PHE ARG SEQRES 10 B 346 GLY LYS MET VAL SER TYR ILE GLN CYS LYS GLU VAL ASP SEQRES 11 B 346 TYR ARG SER ASP ARG ARG GLU ASP TYR TYR ASP ILE GLN SEQRES 12 B 346 LEU SER ILE LYS GLY LYS LYS ASN ILE PHE GLU SER PHE SEQRES 13 B 346 VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP GLY ASP ASN SEQRES 14 B 346 LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN GLU ALA GLU SEQRES 15 B 346 LYS GLY VAL LYS PHE LEU THR LEU PRO PRO VAL LEU HIS SEQRES 16 B 346 LEU GLN LEU MET ARG PHE MET TYR ASP PRO GLN THR ASP SEQRES 17 B 346 GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU PHE PRO GLU SEQRES 18 B 346 GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS THR ASP PRO SEQRES 19 B 346 LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA VAL LEU VAL SEQRES 20 B 346 HIS SER GLY ASP ASN HIS GLY GLY HIS TYR VAL VAL TYR SEQRES 21 B 346 LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS LYS PHE ASP SEQRES 22 B 346 ASP ASP VAL VAL SER ARG CYS THR LYS GLU GLU ALA ILE SEQRES 23 B 346 GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP LEU SER VAL SEQRES 24 B 346 ARG HIS CYS THR ASN ALA TYR MET LEU VAL TYR ILE ARG SEQRES 25 B 346 GLU SER LYS LEU SER GLU VAL LEU GLN ALA VAL THR ASP SEQRES 26 B 346 HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU SEQRES 27 B 346 GLU LYS ARG ILE GLU ALA GLN LYS HET AJJ A 601 19 HET GOL A 602 6 HET AJJ B 601 19 HET GOL B 602 6 HETNAM AJJ 4-[3-(1-METHYLPIPERIDIN-4-YL)-1,2,4-OXADIAZOL-5- HETNAM 2 AJJ YL]PHENOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 AJJ 2(C14 H17 N3 O2) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *55(H2 O) HELIX 1 AA1 TYR A 224 PHE A 234 1 11 HELIX 2 AA2 THR A 235 MET A 244 1 10 HELIX 3 AA3 SER A 255 SER A 270 1 16 HELIX 4 AA4 THR A 276 GLY A 284 1 9 HELIX 5 AA5 ASP A 289 HIS A 294 1 6 HELIX 6 AA6 ASP A 295 MET A 311 1 17 HELIX 7 AA7 GLY A 318 ARG A 325 1 8 HELIX 8 AA8 ASN A 359 VAL A 368 1 10 HELIX 9 AA9 ASP A 374 LYS A 378 5 5 HELIX 10 AB1 GLY A 382 HIS A 384 5 3 HELIX 11 AB2 ASP A 434 LEU A 437 5 4 HELIX 12 AB3 THR A 489 ILE A 494 1 6 HELIX 13 AB4 GLU A 495 TYR A 498 5 4 HELIX 14 AB5 LYS A 523 LEU A 528 1 6 HELIX 15 AB6 THR A 532 ILE A 536 5 5 HELIX 16 AB7 PRO A 537 ALA A 552 1 16 HELIX 17 AB8 TYR B 224 PHE B 234 1 11 HELIX 18 AB9 THR B 235 MET B 244 1 10 HELIX 19 AC1 SER B 255 SER B 270 1 16 HELIX 20 AC2 THR B 276 PHE B 283 1 8 HELIX 21 AC3 ASP B 295 MET B 311 1 17 HELIX 22 AC4 GLY B 318 ARG B 325 1 8 HELIX 23 AC5 ASN B 359 VAL B 368 1 10 HELIX 24 AC6 ASP B 374 LYS B 378 5 5 HELIX 25 AC7 GLY B 382 HIS B 384 5 3 HELIX 26 AC8 ASP B 434 LEU B 437 5 4 HELIX 27 AC9 THR B 489 ILE B 494 1 6 HELIX 28 AD1 GLU B 495 TYR B 498 5 4 HELIX 29 AD2 LYS B 523 LEU B 528 1 6 HELIX 30 AD3 THR B 532 ILE B 536 5 5 HELIX 31 AD4 PRO B 537 LYS B 554 1 18 SHEET 1 AA1 4 ARG A 340 TYR A 347 0 SHEET 2 AA1 4 GLY A 326 CYS A 334 -1 N MET A 328 O GLU A 345 SHEET 3 AA1 4 ALA A 389 PHE A 395 -1 O LYS A 394 N VAL A 329 SHEET 4 AA1 4 GLU A 371 LEU A 373 -1 N GLU A 371 O LYS A 391 SHEET 1 AA2 5 ILE A 350 SER A 353 0 SHEET 2 AA2 5 VAL A 401 MET A 407 1 O GLN A 405 N LEU A 352 SHEET 3 AA2 5 THR A 511 ARG A 520 -1 O TYR A 518 N LEU A 402 SHEET 4 AA2 5 ASN A 447 SER A 457 -1 N HIS A 451 O VAL A 517 SHEET 5 AA2 5 GLN A 430 PRO A 432 -1 N LEU A 431 O TYR A 448 SHEET 1 AA3 7 ILE A 350 SER A 353 0 SHEET 2 AA3 7 VAL A 401 MET A 407 1 O GLN A 405 N LEU A 352 SHEET 3 AA3 7 THR A 511 ARG A 520 -1 O TYR A 518 N LEU A 402 SHEET 4 AA3 7 ASN A 447 SER A 457 -1 N HIS A 451 O VAL A 517 SHEET 5 AA3 7 HIS A 464 LEU A 469 -1 O VAL A 466 N VAL A 455 SHEET 6 AA3 7 CYS A 478 ASP A 481 -1 O PHE A 480 N VAL A 467 SHEET 7 AA3 7 VAL A 484 ARG A 487 -1 O SER A 486 N LYS A 479 SHEET 1 AA4 2 TYR A 379 ASP A 380 0 SHEET 2 AA4 2 LEU A 386 GLN A 387 -1 O GLN A 387 N TYR A 379 SHEET 1 AA5 2 PHE A 409 TYR A 411 0 SHEET 2 AA5 2 ASN A 418 LYS A 420 -1 O ILE A 419 N MET A 410 SHEET 1 AA6 4 ARG B 340 TYR B 347 0 SHEET 2 AA6 4 GLY B 326 CYS B 334 -1 N MET B 328 O GLU B 345 SHEET 3 AA6 4 ALA B 389 THR B 397 -1 O LEU B 396 N LYS B 327 SHEET 4 AA6 4 GLU B 371 LEU B 373 -1 N GLU B 371 O LYS B 391 SHEET 1 AA7 5 ILE B 350 LEU B 352 0 SHEET 2 AA7 5 VAL B 401 LEU B 406 1 O GLN B 405 N LEU B 352 SHEET 3 AA7 5 THR B 511 ARG B 520 -1 O TYR B 518 N LEU B 402 SHEET 4 AA7 5 ASN B 447 SER B 457 -1 N HIS B 451 O VAL B 517 SHEET 5 AA7 5 GLN B 430 PRO B 432 -1 N LEU B 431 O TYR B 448 SHEET 1 AA8 7 ILE B 350 LEU B 352 0 SHEET 2 AA8 7 VAL B 401 LEU B 406 1 O GLN B 405 N LEU B 352 SHEET 3 AA8 7 THR B 511 ARG B 520 -1 O TYR B 518 N LEU B 402 SHEET 4 AA8 7 ASN B 447 SER B 457 -1 N HIS B 451 O VAL B 517 SHEET 5 AA8 7 HIS B 464 LEU B 469 -1 O VAL B 466 N VAL B 455 SHEET 6 AA8 7 TRP B 477 ASP B 481 -1 O CYS B 478 N LEU B 469 SHEET 7 AA8 7 VAL B 484 CYS B 488 -1 O SER B 486 N LYS B 479 SHEET 1 AA9 2 TYR B 379 ASP B 380 0 SHEET 2 AA9 2 LEU B 386 GLN B 387 -1 O GLN B 387 N TYR B 379 SHEET 1 AB1 2 TYR B 411 ASP B 412 0 SHEET 2 AB1 2 GLN B 417 ASN B 418 -1 O GLN B 417 N ASP B 412 CISPEP 1 PRO A 413 GLN A 414 0 -7.63 CISPEP 2 GLN B 414 THR B 415 0 -1.24 SITE 1 AC1 7 CYS A 300 ARG A 301 LEU A 304 ASP A 305 SITE 2 AC1 7 TYR A 348 ASP A 349 HIS A 403 SITE 1 AC2 6 TYR A 224 ASP A 295 VAL A 296 PHE A 409 SITE 2 AC2 6 TYR A 465 TYR A 514 SITE 1 AC3 7 CYS B 300 ARG B 301 LEU B 304 ASP B 305 SITE 2 AC3 7 TYR B 348 ASP B 349 HIS B 403 SITE 1 AC4 5 TYR B 224 ASP B 295 VAL B 296 TYR B 465 SITE 2 AC4 5 TYR B 514 CRYST1 76.292 69.279 77.070 90.00 95.00 90.00 P 1 21 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 0.013108 0.000000 0.001148 0.00000 SCALE2 0.000000 0.014434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013025 0.00000