HEADER HYDROLASE 27-FEB-17 5N9R TITLE CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH A POTENT, SELECTIVE AND TITLE 2 REVERSIBLE SMALL-MOLECULE INHIBITOR 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 USP7, REVERSIBLE, INHIBITOR, SELECTIVE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.HARRISON,G.GAVORY,C.O'DOWD,M.HELM,I.FLASZ,E.ARKOUDIS,A.DOSSANG, AUTHOR 2 C.HUGHES,E.CASSIDY,K.MCCLELLAND,E.ODRZYWOL,N.PAGE,O.BARKER,H.MIEL REVDAT 4 17-JAN-24 5N9R 1 REMARK REVDAT 3 24-JAN-18 5N9R 1 JRNL REVDAT 2 13-DEC-17 5N9R 1 JRNL REVDAT 1 06-DEC-17 5N9R 0 JRNL AUTH G.GAVORY,C.R.O'DOWD,M.D.HELM,J.FLASZ,E.ARKOUDIS,A.DOSSANG, JRNL AUTH 2 C.HUGHES,E.CASSIDY,K.MCCLELLAND,E.ODRZYWOL,N.PAGE,O.BARKER, JRNL AUTH 3 H.MIEL,T.HARRISON JRNL TITL DISCOVERY AND CHARACTERIZATION OF HIGHLY POTENT AND JRNL TITL 2 SELECTIVE ALLOSTERIC USP7 INHIBITORS. JRNL REF NAT. CHEM. BIOL. V. 14 118 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 29200206 JRNL DOI 10.1038/NCHEMBIO.2528 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 35975 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1848 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) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5720 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 528 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.99000 REMARK 3 B22 (A**2) : -0.51000 REMARK 3 B33 (A**2) : -1.84000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.269 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.416 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5988 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5434 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8086 ; 1.378 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12696 ; 0.987 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 716 ; 6.235 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;40.437 ;24.951 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1094 ;17.118 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;16.086 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 861 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6595 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1176 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 207 A 562 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0270 13.4420 0.7250 REMARK 3 T TENSOR REMARK 3 T11: 0.0872 T22: 0.0718 REMARK 3 T33: 0.0485 T12: 0.0457 REMARK 3 T13: 0.0197 T23: -0.0000 REMARK 3 L TENSOR REMARK 3 L11: 2.3177 L22: 1.5685 REMARK 3 L33: 0.3811 L12: 0.6165 REMARK 3 L13: -0.2264 L23: -0.0810 REMARK 3 S TENSOR REMARK 3 S11: -0.0157 S12: 0.0630 S13: -0.1716 REMARK 3 S21: 0.1779 S22: 0.0246 S23: -0.1593 REMARK 3 S31: -0.1215 S32: -0.1623 S33: -0.0089 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 207 B 552 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6830 11.6920 36.4280 REMARK 3 T TENSOR REMARK 3 T11: 0.0895 T22: 0.0241 REMARK 3 T33: 0.0243 T12: -0.0414 REMARK 3 T13: 0.0287 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 2.4358 L22: 1.4802 REMARK 3 L33: 1.5863 L12: 0.5193 REMARK 3 L13: 0.1966 L23: -0.2689 REMARK 3 S TENSOR REMARK 3 S11: 0.0540 S12: 0.0485 S13: 0.0066 REMARK 3 S21: 0.1064 S22: 0.0202 S23: 0.1421 REMARK 3 S31: -0.0862 S32: 0.0586 S33: -0.0742 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 4 REMARK 4 5N9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003677. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36846 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 : 4.500 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 (%): 48.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, LI2-SULFATE., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 33.47000 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 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 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 ASP A 503 REMARK 465 GLN B 553 REMARK 465 LYS B 554 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 465 HIS B 561 REMARK 465 HIS B 562 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 -109.47 56.42 REMARK 500 PHE A 409 76.08 -100.16 REMARK 500 ASP A 482 -111.46 46.78 REMARK 500 ILE A 494 -83.48 -105.99 REMARK 500 CYS B 223 -115.43 55.41 REMARK 500 SER B 252 -39.50 -35.40 REMARK 500 ASP B 482 -110.53 49.30 REMARK 500 ILE B 494 -82.30 -110.88 REMARK 500 HIS B 501 54.95 -92.04 REMARK 500 GLU B 551 59.54 -91.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1393 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1394 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A1395 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH B1331 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH B1332 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH B1333 DISTANCE = 6.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8RN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8RN B 1006 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5N9T RELATED DB: PDB REMARK 900 59NT CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND DBREF 5N9R A 207 560 UNP Q93009 UBP7_HUMAN 207 560 DBREF 5N9R B 207 560 UNP Q93009 UBP7_HUMAN 207 560 SEQADV 5N9R MET A 206 UNP Q93009 INITIATING METHIONINE SEQADV 5N9R HIS A 561 UNP Q93009 EXPRESSION TAG SEQADV 5N9R HIS A 562 UNP Q93009 EXPRESSION TAG SEQADV 5N9R MET B 206 UNP Q93009 INITIATING METHIONINE SEQADV 5N9R HIS B 561 UNP Q93009 EXPRESSION TAG SEQADV 5N9R HIS B 562 UNP Q93009 EXPRESSION TAG SEQRES 1 A 357 MET SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 A 357 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 A 357 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 A 357 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 A 357 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 A 357 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 A 357 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 A 357 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 A 357 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 A 357 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 A 357 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 A 357 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 A 357 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 A 357 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 A 357 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 A 357 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 A 357 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 A 357 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 A 357 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 A 357 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 A 357 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 A 357 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 A 357 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 A 357 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 A 357 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 A 357 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 A 357 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 A 357 GLU ARG GLN GLU HIS HIS SEQRES 1 B 357 MET SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN SEQRES 2 B 357 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR SEQRES 3 B 357 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET SEQRES 4 B 357 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO SEQRES 5 B 357 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER SEQRES 6 B 357 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE SEQRES 7 B 357 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL SEQRES 8 B 357 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN SEQRES 9 B 357 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS SEQRES 10 B 357 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS SEQRES 11 B 357 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR SEQRES 12 B 357 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE SEQRES 13 B 357 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP SEQRES 14 B 357 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN SEQRES 15 B 357 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO SEQRES 16 B 357 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO SEQRES 17 B 357 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU SEQRES 18 B 357 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS SEQRES 19 B 357 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA SEQRES 20 B 357 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR SEQRES 21 B 357 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS SEQRES 22 B 357 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU SEQRES 23 B 357 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP SEQRES 24 B 357 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL SEQRES 25 B 357 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA SEQRES 26 B 357 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG SEQRES 27 B 357 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS SEQRES 28 B 357 GLU ARG GLN GLU HIS HIS HET SO4 A1001 5 HET GOL A1002 6 HET 8RN A1003 30 HET SO4 B1001 5 HET SO4 B1002 5 HET DMS B1003 4 HET GOL B1004 6 HET GOL B1005 6 HET 8RN B1006 30 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM 8RN 7-BROMANYL-3-[[4-OXIDANYL-1-[(3~{R})-3- HETNAM 2 8RN PHENYLBUTANOYL]PIPERIDIN-4-YL]METHYL]THIENO[3,2- HETNAM 3 8RN D]PYRIMIDIN-4-ONE HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 5 8RN 2(C22 H24 BR N3 O3 S) FORMUL 8 DMS C2 H6 O S FORMUL 12 HOH *528(H2 O) HELIX 1 AA1 MET A 206 GLY A 212 1 7 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 MET A 311 1 17 HELIX 8 AA8 GLY A 318 ARG A 325 1 8 HELIX 9 AA9 ASN A 359 VAL A 368 1 10 HELIX 10 AB1 ASP A 374 LYS A 378 5 5 HELIX 11 AB2 GLY A 382 HIS A 384 5 3 HELIX 12 AB3 ASP A 434 LEU A 437 5 4 HELIX 13 AB4 THR A 489 ILE A 494 1 6 HELIX 14 AB5 GLU A 495 TYR A 498 5 4 HELIX 15 AB6 LYS A 523 LEU A 528 1 6 HELIX 16 AB7 THR A 532 ILE A 536 5 5 HELIX 17 AB8 PRO A 537 HIS A 562 1 26 HELIX 18 AB9 SER B 207 THR B 211 1 5 HELIX 19 AC1 TYR B 224 PHE B 234 1 11 HELIX 20 AC2 THR B 235 MET B 245 1 11 HELIX 21 AC3 SER B 255 SER B 270 1 16 HELIX 22 AC4 THR B 276 PHE B 283 1 8 HELIX 23 AC5 THR B 287 GLN B 293 1 7 HELIX 24 AC6 ASP B 295 MET B 311 1 17 HELIX 25 AC7 GLY B 318 ARG B 325 1 8 HELIX 26 AC8 ASN B 359 VAL B 368 1 10 HELIX 27 AC9 ASP B 374 LYS B 378 5 5 HELIX 28 AD1 GLY B 382 HIS B 384 5 3 HELIX 29 AD2 PRO B 413 ASP B 416 5 4 HELIX 30 AD3 ASP B 434 LEU B 437 5 4 HELIX 31 AD4 THR B 489 ILE B 494 1 6 HELIX 32 AD5 GLU B 495 TYR B 498 5 4 HELIX 33 AD6 LYS B 523 LEU B 528 1 6 HELIX 34 AD7 THR B 532 ILE B 536 5 5 HELIX 35 AD8 PRO B 537 GLU B 551 1 15 SHEET 1 AA1 4 ARG A 340 TYR A 347 0 SHEET 2 AA1 4 GLY A 326 CYS A 334 -1 N SER A 330 O ARG A 343 SHEET 3 AA1 4 ALA A 389 THR A 397 -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 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 THR A 511 ARG A 520 -1 O TYR A 514 N LEU A 406 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 THR A 511 ARG A 520 -1 O TYR A 514 N LEU A 406 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 TRP A 477 ASP A 481 -1 O PHE A 480 N VAL A 467 SHEET 7 AA3 7 VAL A 484 CYS A 488 -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 GLN A 417 N ASP A 412 SHEET 1 AA6 4 ARG B 343 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 LEU B 373 O ALA B 389 SHEET 1 AA7 5 ILE B 350 SER B 353 0 SHEET 2 AA7 5 VAL B 401 MET B 407 1 O GLN B 405 N LEU B 352 SHEET 3 AA7 5 THR B 511 ARG B 520 -1 O LEU B 516 N LEU B 404 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 SER B 353 0 SHEET 2 AA8 7 VAL B 401 MET B 407 1 O GLN B 405 N LEU B 352 SHEET 3 AA8 7 THR B 511 ARG B 520 -1 O LEU B 516 N LEU B 404 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 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 PHE B 409 ASP B 412 0 SHEET 2 AB1 2 GLN B 417 LYS B 420 -1 O ILE B 419 N MET B 410 SITE 1 AC1 8 GLN A 219 ARG A 262 GLY A 275 THR A 276 SITE 2 AC1 8 LYS A 277 LYS A 278 HOH A1120 HOH A1180 SITE 1 AC2 5 SER A 330 TYR A 331 SER A 341 ARG A 343 SITE 2 AC2 5 HOH A1197 SITE 1 AC3 14 TYR A 224 ASP A 295 VAL A 296 GLN A 297 SITE 2 AC3 14 LEU A 406 MET A 407 ARG A 408 PHE A 409 SITE 3 AC3 14 LYS A 420 HIS A 456 ASN A 460 HIS A 461 SITE 4 AC3 14 TYR A 465 TYR A 514 SITE 1 AC4 7 GLY B 275 THR B 276 LYS B 277 LYS B 278 SITE 2 AC4 7 HOH B1101 HOH B1153 HOH B1201 SITE 1 AC5 4 THR B 489 LYS B 490 GLU B 491 HOH B1152 SITE 1 AC6 5 ASP B 295 PHE B 409 ASN B 418 8RN B1006 SITE 2 AC6 5 HOH B1139 SITE 1 AC7 6 GLN B 297 ARG B 301 ASP B 349 GLN B 351 SITE 2 AC7 6 HOH B1148 HOH B1216 SITE 1 AC8 6 PHE B 234 ARG B 239 ALA B 530 VAL B 531 SITE 2 AC8 6 HOH B1164 HOH B1199 SITE 1 AC9 16 TYR B 224 ASP B 295 VAL B 296 GLN B 297 SITE 2 AC9 16 LEU B 406 MET B 407 ARG B 408 PHE B 409 SITE 3 AC9 16 MET B 410 LYS B 420 HIS B 456 ASN B 460 SITE 4 AC9 16 HIS B 461 TYR B 465 TYR B 514 DMS B1003 CRYST1 74.940 66.940 81.090 90.00 105.09 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 0.013344 0.000000 0.003598 0.00000 SCALE2 0.000000 0.014939 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012772 0.00000