HEADER HYDROLASE 17-MAR-17 5NGE TITLE CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH THE NON-COVALENT INHIBITOR, TITLE 2 FT671 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 5 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- COMPND 6 PROCESSING PROTEASE 7; COMPND 7 EC: 3.4.19.12; COMPND 8 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: 562 KEYWDS DEUBIQUITINATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.P.TURNBULL,W.W.KRAJEWSKI,S.IOANNIDIS,B.M.KESSLER,D.KOMANDER REVDAT 5 17-JAN-24 5NGE 1 REMARK REVDAT 4 08-NOV-17 5NGE 1 JRNL REVDAT 3 01-NOV-17 5NGE 1 JRNL REVDAT 2 25-OCT-17 5NGE 1 TITLE REVDAT 1 18-OCT-17 5NGE 0 JRNL AUTH A.P.TURNBULL,S.IOANNIDIS,W.W.KRAJEWSKI,A.PINTO-FERNANDEZ, JRNL AUTH 2 C.HERIDE,A.C.L.MARTIN,L.M.TONKIN,E.C.TOWNSEND,S.M.BUKER, JRNL AUTH 3 D.R.LANCIA,J.A.CARAVELLA,A.V.TOMS,T.M.CHARLTON, JRNL AUTH 4 J.LAHDENRANTA,E.WILKER,B.C.FOLLOWS,N.J.EVANS,L.STEAD,C.ALLI, JRNL AUTH 5 V.V.ZARAYSKIY,A.C.TALBOT,A.J.BUCKMELTER,M.WANG,C.L.MCKINNON, JRNL AUTH 6 F.SAAB,J.F.MCGOURAN,H.CENTURY,M.GERSCH,M.S.PITTMAN, JRNL AUTH 7 C.G.MARSHALL,T.M.RAYNHAM,M.SIMCOX,L.M.D.STEWART, JRNL AUTH 8 S.B.MCLOUGHLIN,J.A.ESCOBEDO,K.W.BAIR,C.J.DINSMORE, JRNL AUTH 9 T.R.HAMMONDS,S.KIM,S.URBE,M.J.CLAGUE,B.M.KESSLER,D.KOMANDER JRNL TITL MOLECULAR BASIS OF USP7 INHIBITION BY SELECTIVE JRNL TITL 2 SMALL-MOLECULE INHIBITORS. JRNL REF NATURE V. 550 481 2017 JRNL REFN ESSN 1476-4687 JRNL PMID 29045389 JRNL DOI 10.1038/NATURE24451 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 29654 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) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1551 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2201 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 48 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60000 REMARK 3 B22 (A**2) : 1.21000 REMARK 3 B33 (A**2) : -2.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.389 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.274 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.216 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.066 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5199 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4657 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7079 ; 1.574 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10662 ; 1.056 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 648 ; 6.192 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 238 ;38.225 ;24.622 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 798 ;16.853 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 786 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5964 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1198 ; 0.004 ; 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): 2598 ; 2.482 ; 3.710 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2597 ; 2.482 ; 3.709 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3238 ; 3.600 ; 5.555 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3239 ; 3.600 ; 5.555 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2601 ; 2.988 ; 3.902 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2602 ; 2.987 ; 3.903 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3840 ; 4.371 ; 5.775 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5631 ; 6.042 ;29.963 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5630 ; 6.042 ;29.958 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 212 554 B 212 554 16760 0.09 0.05 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 212 A 556 REMARK 3 ORIGIN FOR THE GROUP (A): 72.4465 -44.3142 80.3985 REMARK 3 T TENSOR REMARK 3 T11: 0.0458 T22: 0.0792 REMARK 3 T33: 0.0334 T12: -0.0217 REMARK 3 T13: 0.0318 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 3.1226 L22: 3.6756 REMARK 3 L33: 1.6073 L12: 0.8717 REMARK 3 L13: 0.0800 L23: 0.4306 REMARK 3 S TENSOR REMARK 3 S11: 0.0163 S12: -0.3638 S13: -0.1254 REMARK 3 S21: 0.2265 S22: -0.0166 S23: 0.1758 REMARK 3 S31: 0.0253 S32: -0.0441 S33: 0.0003 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 210 B 554 REMARK 3 ORIGIN FOR THE GROUP (A): 91.5345 -45.8211 43.6650 REMARK 3 T TENSOR REMARK 3 T11: 0.1103 T22: 0.0571 REMARK 3 T33: 0.0255 T12: 0.0377 REMARK 3 T13: 0.0208 T23: 0.0009 REMARK 3 L TENSOR REMARK 3 L11: 2.6082 L22: 3.5104 REMARK 3 L33: 4.4121 L12: -0.7701 REMARK 3 L13: 0.1395 L23: -0.4776 REMARK 3 S TENSOR REMARK 3 S11: 0.1282 S12: 0.3070 S13: -0.1472 REMARK 3 S21: -0.2793 S22: -0.1199 S23: 0.0324 REMARK 3 S31: 0.2596 S32: -0.0239 S33: -0.0083 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 5NGE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200004046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 77.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.71900 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 (%): 48.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) POLYETHYLENE GLYCOL (PEG) REMARK 280 1500, 100 MM MMT PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 35.15000 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 GLY A 206 REMARK 465 SER A 207 REMARK 465 LYS A 208 REMARK 465 LYS A 209 REMARK 465 HIS A 210 REMARK 465 THR A 211 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 A 509 REMARK 465 GLU A 557 REMARK 465 ARG A 558 REMARK 465 GLN A 559 REMARK 465 GLU A 560 REMARK 465 GLY B 206 REMARK 465 SER B 207 REMARK 465 LYS B 208 REMARK 465 LYS B 209 REMARK 465 ILE B 332 REMARK 465 GLN B 333 REMARK 465 CYS B 334 REMARK 465 LYS B 335 REMARK 465 GLU B 336 REMARK 465 VAL B 337 REMARK 465 ASP B 338 REMARK 465 TYR B 339 REMARK 465 ARG B 340 REMARK 465 GLN B 372 REMARK 465 LEU B 373 REMARK 465 ASP B 374 REMARK 465 GLY B 375 REMARK 465 ASP B 376 REMARK 465 ASN B 377 REMARK 465 LYS B 378 REMARK 465 TYR B 379 REMARK 465 ASP B 380 REMARK 465 ALA B 381 REMARK 465 GLY B 382 REMARK 465 GLU B 383 REMARK 465 HIS B 384 REMARK 465 GLY B 385 REMARK 465 LEU B 386 REMARK 465 GLN B 387 REMARK 465 GLU B 388 REMARK 465 ALA B 389 REMARK 465 GLU B 390 REMARK 465 ASP B 502 REMARK 465 ASP B 503 REMARK 465 ASP B 504 REMARK 465 LEU B 505 REMARK 465 ARG B 555 REMARK 465 LYS B 556 REMARK 465 GLU B 557 REMARK 465 ARG B 558 REMARK 465 GLN B 559 REMARK 465 GLU B 560 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 A 217 CD CE NZ REMARK 470 LYS A 272 CG CD CE NZ REMARK 470 LYS A 277 CG CD CE NZ REMARK 470 LYS A 281 CE NZ REMARK 470 LEU A 288 CG CD1 CD2 REMARK 470 GLN A 293 CG CD OE1 NE2 REMARK 470 LYS A 322 CE NZ REMARK 470 LYS A 327 CE NZ REMARK 470 LYS A 335 CD CE NZ REMARK 470 ARG A 344 CD NE CZ NH1 NH2 REMARK 470 LYS A 355 CE NZ REMARK 470 LYS A 358 CG CD CE NZ REMARK 470 GLU A 371 CD OE1 OE2 REMARK 470 ASN A 377 CG OD1 ND2 REMARK 470 LYS A 378 CD CE NZ REMARK 470 GLU A 383 CD OE1 OE2 REMARK 470 LEU A 386 CD1 CD2 REMARK 470 GLU A 388 CG CD OE1 OE2 REMARK 470 LYS A 391 CD CE NZ REMARK 470 LYS A 394 CD CE NZ REMARK 470 TYR A 411 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 414 CG CD OE1 NE2 REMARK 470 ASP A 416 CG OD1 OD2 REMARK 470 GLN A 417 CG CD OE1 NE2 REMARK 470 ASN A 418 CG OD1 ND2 REMARK 470 LYS A 439 CE NZ REMARK 470 LYS A 443 CG CD CE NZ REMARK 470 ASP A 459 CG OD1 OD2 REMARK 470 LYS A 472 CE NZ REMARK 470 LYS A 476 CE NZ REMARK 470 ARG A 487 NE CZ NH1 NH2 REMARK 470 HIS A 501 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 538 CG CD OE1 NE2 REMARK 470 GLN A 539 CD OE1 NE2 REMARK 470 GLU A 542 CG CD OE1 OE2 REMARK 470 LYS A 548 CG CD CE NZ REMARK 470 GLU A 551 CG CD OE1 OE2 REMARK 470 LYS A 554 CG CD CE NZ REMARK 470 ARG A 555 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 556 CG CD CE NZ REMARK 470 LYS B 217 CG CD CE NZ REMARK 470 GLN B 219 CG CD OE1 NE2 REMARK 470 LYS B 254 CG CD CE NZ REMARK 470 ASP B 271 CG OD1 OD2 REMARK 470 LYS B 272 CG CD CE NZ REMARK 470 LYS B 277 CG CD CE NZ REMARK 470 LYS B 281 CD CE NZ REMARK 470 GLN B 293 CG CD OE1 NE2 REMARK 470 LYS B 310 CE NZ REMARK 470 LYS B 322 CD CE NZ REMARK 470 LYS B 327 CD CE NZ REMARK 470 SER B 341 OG REMARK 470 ARG B 344 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 345 CG CD OE1 OE2 REMARK 470 LYS B 355 CG CD CE NZ REMARK 470 LYS B 357 CE NZ REMARK 470 LYS B 358 CG CD CE NZ REMARK 470 GLU B 371 CG CD OE1 OE2 REMARK 470 LYS B 394 CG CD CE NZ REMARK 470 GLN B 414 CG CD OE1 NE2 REMARK 470 GLN B 417 CG CD OE1 NE2 REMARK 470 LYS B 439 CG CD CE NZ REMARK 470 LYS B 443 CE NZ REMARK 470 ASP B 459 CG OD1 OD2 REMARK 470 LYS B 476 CG CD CE NZ REMARK 470 LYS B 479 CG CD CE NZ REMARK 470 ARG B 487 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 490 CD CE NZ REMARK 470 GLU B 491 CG CD OE1 OE2 REMARK 470 GLU B 495 CG CD OE1 OE2 REMARK 470 ARG B 508 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 534 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 538 CG CD OE1 NE2 REMARK 470 GLN B 539 CD OE1 NE2 REMARK 470 GLU B 542 CG CD OE1 OE2 REMARK 470 LEU B 544 CG CD1 CD2 REMARK 470 GLN B 545 CG CD OE1 NE2 REMARK 470 GLU B 546 CG CD OE1 OE2 REMARK 470 LYS B 548 CD CE NZ REMARK 470 GLU B 551 CG CD OE1 OE2 REMARK 470 GLN B 553 CD OE1 NE2 REMARK 470 LYS B 554 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 OE1 GLU A 308 O HOH A 701 1.93 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 CYS A 223 -110.38 43.48 REMARK 500 GLU A 248 -34.32 -38.47 REMARK 500 SER A 252 -31.06 -37.49 REMARK 500 TRP A 285 79.90 -107.86 REMARK 500 LYS A 378 153.25 -48.60 REMARK 500 ASP A 416 72.57 30.08 REMARK 500 ASP A 482 -111.06 51.11 REMARK 500 ILE A 494 -84.93 -94.43 REMARK 500 GLN B 219 48.24 -140.04 REMARK 500 CYS B 223 -109.40 44.90 REMARK 500 GLU B 248 -34.29 -39.51 REMARK 500 SER B 252 -30.28 -35.87 REMARK 500 PRO B 273 150.10 -49.91 REMARK 500 TRP B 285 54.31 -103.18 REMARK 500 ASP B 416 71.13 31.75 REMARK 500 ASP B 482 -111.13 50.60 REMARK 500 ILE B 494 -83.96 -97.48 REMARK 500 ALA B 552 -3.03 -56.00 REMARK 500 GLN B 553 72.45 -105.23 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 8WK A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8WK B 601 DBREF 5NGE A 208 560 UNP Q93009 UBP7_HUMAN 192 544 DBREF 5NGE B 208 560 UNP Q93009 UBP7_HUMAN 192 544 SEQADV 5NGE GLY A 206 UNP Q93009 EXPRESSION TAG SEQADV 5NGE SER A 207 UNP Q93009 EXPRESSION TAG SEQADV 5NGE GLY B 206 UNP Q93009 EXPRESSION TAG SEQADV 5NGE SER B 207 UNP Q93009 EXPRESSION TAG SEQRES 1 A 355 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 A 355 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 A 355 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 A 355 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 A 355 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 A 355 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 A 355 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 A 355 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 A 355 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 A 355 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 A 355 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 A 355 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 A 355 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 A 355 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 A 355 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 A 355 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 A 355 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 A 355 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 A 355 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 A 355 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 A 355 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 A 355 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 A 355 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 A 355 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 A 355 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 A 355 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 A 355 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 A 355 GLU ARG GLN GLU SEQRES 1 B 355 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 B 355 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 B 355 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 B 355 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 B 355 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 B 355 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 B 355 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 B 355 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 B 355 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 B 355 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 B 355 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 B 355 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 B 355 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 B 355 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 B 355 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 B 355 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 B 355 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 B 355 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 B 355 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 B 355 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 B 355 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 B 355 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 B 355 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 B 355 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 B 355 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 B 355 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 B 355 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 B 355 GLU ARG GLN GLU HET 8WK A 601 38 HET 8WK B 601 38 HETNAM 8WK 5-[[1-[(3~{S})-4,4-BIS(FLUORANYL)-3-(3- HETNAM 2 8WK FLUORANYLPYRAZOL-1-YL)BUTANOYL]-4-OXIDANYL-PIPERIDIN- HETNAM 3 8WK 4-YL]METHYL]-1-(4-FLUOROPHENYL)PYRAZOLO[3,4- HETNAM 4 8WK D]PYRIMIDIN-4-ONE FORMUL 3 8WK 2(C24 H23 F4 N7 O3) FORMUL 5 HOH *48(H2 O) HELIX 1 AA1 GLN A 219 CYS A 223 5 5 HELIX 2 AA2 TYR A 224 PHE A 234 1 11 HELIX 3 AA3 THR A 235 MET A 244 1 10 HELIX 4 AA4 SER A 255 SER A 270 1 16 HELIX 5 AA5 THR A 276 GLY A 284 1 9 HELIX 6 AA6 THR A 287 GLN A 293 1 7 HELIX 7 AA7 ASP A 295 LYS A 312 1 18 HELIX 8 AA8 GLY A 318 ARG A 325 1 8 HELIX 9 AA9 ASN A 359 ALA A 369 1 11 HELIX 10 AB1 ASP A 374 LYS A 378 5 5 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 LYS A 556 1 20 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 GLY B 284 1 9 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 ALA B 369 1 11 HELIX 24 AC6 ASP B 434 LEU B 437 5 4 HELIX 25 AC7 THR B 489 ILE B 494 1 6 HELIX 26 AC8 GLU B 495 TYR B 498 5 4 HELIX 27 AC9 LYS B 523 LEU B 528 1 6 HELIX 28 AD1 THR B 532 ILE B 536 5 5 HELIX 29 AD2 PRO B 537 ALA B 552 1 16 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 THR A 397 -1 O GLU A 390 N GLN A 333 SHEET 4 AA1 4 GLU A 371 LEU A 373 -1 N LEU A 373 O ALA A 389 SHEET 1 AA2 5 ILE A 350 LEU A 352 0 SHEET 2 AA2 5 VAL A 401 LEU A 406 1 O GLN A 405 N LEU A 352 SHEET 3 AA2 5 ASN A 512 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 LEU A 352 0 SHEET 2 AA3 7 VAL A 401 LEU A 406 1 O GLN A 405 N LEU A 352 SHEET 3 AA3 7 ASN A 512 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 ASP A 412 0 SHEET 2 AA5 2 GLN A 417 LYS A 420 -1 O ILE A 419 N MET A 410 SHEET 1 AA6 3 ARG B 343 TYR B 347 0 SHEET 2 AA6 3 GLY B 326 TYR B 331 -1 N SER B 330 O ARG B 343 SHEET 3 AA6 3 GLY B 392 THR B 397 -1 O LYS B 394 N VAL B 329 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 ASN B 512 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 ASN B 512 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 CYS B 478 ASP B 481 -1 O PHE B 480 N VAL B 467 SHEET 7 AA8 7 VAL B 484 ARG B 487 -1 O SER B 486 N LYS B 479 SHEET 1 AA9 2 PHE B 409 ASP B 412 0 SHEET 2 AA9 2 GLN B 417 LYS B 420 -1 O ILE B 419 N MET B 410 SSBOND 1 CYS A 315 CYS B 315 1555 1555 2.09 SITE 1 AC1 14 TYR A 224 ASP A 295 VAL A 296 GLN A 297 SITE 2 AC1 14 LEU A 406 MET A 407 ARG A 408 PHE A 409 SITE 3 AC1 14 HIS A 456 ASP A 459 ASN A 460 HIS A 461 SITE 4 AC1 14 TYR A 465 TYR A 514 SITE 1 AC2 14 ASP B 295 VAL B 296 GLN B 297 LEU B 406 SITE 2 AC2 14 MET B 407 ARG B 408 PHE B 409 LYS B 420 SITE 3 AC2 14 HIS B 456 ASP B 459 ASN B 460 HIS B 461 SITE 4 AC2 14 TYR B 465 TYR B 514 CRYST1 71.280 70.300 78.560 90.00 97.17 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 0.014029 0.000000 0.001765 0.00000 SCALE2 0.000000 0.014225 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012829 0.00000