HEADER HYDROLASE 01-DEC-17 6F5H TITLE CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH A 4-HYDROXYPIPERIDINE BASED TITLE 2 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,J.FLASZ,A.DOSSANG,C.HUGHES, AUTHOR 2 E.CASSIDY,K.MCCLELLAND,E.ODRZYWOL,N.PAGE,O.BARKER,H.MIEL,S.FEUTRON- AUTHOR 3 BURTON,J.S.S.ROUNTREE REVDAT 1 11-APR-18 6F5H 0 JRNL AUTH C.R.O'DOWD,M.D.HELM,J.S.S.ROUNTREE,J.T.FLASZ,E.ARKOUDIS, JRNL AUTH 2 H.MIEL,P.R.HEWITT,L.JORDAN,O.BARKER,C.HUGHES,E.ROZYCKA, JRNL AUTH 3 E.CASSIDY,K.MCCLELLAND,E.ODRZYWOL,N.PAGE,S.FEUTREN-BURTON, JRNL AUTH 4 S.DVORKIN,G.GAVORY,T.HARRISON JRNL TITL IDENTIFICATION AND STRUCTURE-GUIDED DEVELOPMENT OF JRNL TITL 2 PYRIMIDINONE BASED USP7 INHIBITORS. JRNL REF ACS MED CHEM LETT V. 9 238 2018 JRNL REFN ISSN 1948-5875 JRNL PMID 29541367 JRNL DOI 10.1021/ACSMEDCHEMLETT.7B00512 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 37973 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1958 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) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2771 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5600 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 404 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.46000 REMARK 3 B22 (A**2) : -2.49000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.78000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.304 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.235 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.221 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.096 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5811 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5278 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7834 ; 1.370 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12325 ; 0.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 683 ; 6.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;39.846 ;24.916 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1054 ;16.826 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;14.168 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 829 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6386 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1147 ; 0.002 ; 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 555 REMARK 3 ORIGIN FOR THE GROUP (A): 26.6000 13.2850 1.2460 REMARK 3 T TENSOR REMARK 3 T11: 0.1306 T22: 0.3219 REMARK 3 T33: 0.0862 T12: -0.0098 REMARK 3 T13: 0.0932 T23: 0.0049 REMARK 3 L TENSOR REMARK 3 L11: 2.2467 L22: 1.5462 REMARK 3 L33: 0.8216 L12: 0.4768 REMARK 3 L13: 0.0062 L23: -0.0234 REMARK 3 S TENSOR REMARK 3 S11: -0.0028 S12: 0.0503 S13: -0.1302 REMARK 3 S21: 0.0715 S22: 0.0010 S23: -0.1005 REMARK 3 S31: -0.0301 S32: -0.0522 S33: 0.0019 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 208 B 551 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6940 12.0420 35.7980 REMARK 3 T TENSOR REMARK 3 T11: 0.1504 T22: 0.3778 REMARK 3 T33: 0.0898 T12: -0.0139 REMARK 3 T13: 0.1088 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 2.2948 L22: 1.8392 REMARK 3 L33: 1.6976 L12: 0.4363 REMARK 3 L13: 0.3811 L23: -0.0646 REMARK 3 S TENSOR REMARK 3 S11: 0.0592 S12: 0.0082 S13: 0.0001 REMARK 3 S21: 0.0514 S22: -0.0021 S23: 0.1621 REMARK 3 S31: -0.0333 S32: -0.0675 S33: -0.0570 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6F5H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JAN-15 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.965 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39952 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 29.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, TRIS, LI2-SULFATE, PH 7.75, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 33.66400 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 SER B 207 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 465 ALA B 552 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 465 HIS B 563 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 OD2 ASP B 250 O HOH B 1101 2.18 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 -102.43 54.13 REMARK 500 THR A 247 34.30 -91.43 REMARK 500 ASN A 377 59.92 -90.21 REMARK 500 ALA A 381 31.99 -97.65 REMARK 500 ASP A 416 53.78 33.00 REMARK 500 ASN A 470 78.33 -110.05 REMARK 500 ASP A 482 -113.10 58.95 REMARK 500 ILE A 494 -89.30 -101.21 REMARK 500 CYS B 223 -103.79 57.88 REMARK 500 SER B 341 45.55 -146.42 REMARK 500 ASN B 377 58.94 -106.88 REMARK 500 GLN B 438 -73.66 -65.03 REMARK 500 ASN B 470 79.82 -112.55 REMARK 500 ASP B 481 77.51 -115.34 REMARK 500 ASP B 482 -115.84 52.47 REMARK 500 ILE B 494 -81.33 -112.22 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 CYS B 510 THR B 511 -143.96 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 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 CQ5 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 CQ5 B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5N9R RELATED DB: PDB REMARK 900 5N9R CONTAINS THE SAME PROTEIN COMPLEXED WITH A RELATED LIGAND. REMARK 900 RELATED ID: 5N9T RELATED DB: PDB REMARK 900 5N9T CONTAINS THE SAME PROTEIN COMPLEXED WITH A RELATED LIGAND. DBREF 6F5H A 207 560 UNP Q93009 UBP7_HUMAN 207 560 DBREF 6F5H B 207 560 UNP Q93009 UBP7_HUMAN 207 560 SEQADV 6F5H HIS A 561 UNP Q93009 EXPRESSION TAG SEQADV 6F5H HIS A 562 UNP Q93009 EXPRESSION TAG SEQADV 6F5H HIS A 563 UNP Q93009 EXPRESSION TAG SEQADV 6F5H HIS B 561 UNP Q93009 EXPRESSION TAG SEQADV 6F5H HIS B 562 UNP Q93009 EXPRESSION TAG SEQADV 6F5H HIS B 563 UNP Q93009 EXPRESSION TAG SEQRES 1 A 357 SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN GLN SEQRES 2 A 357 GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR LEU SEQRES 3 A 357 PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET MET SEQRES 4 A 357 PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO LEU SEQRES 5 A 357 ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER ASP SEQRES 6 A 357 LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE GLY SEQRES 7 A 357 TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL GLN SEQRES 8 A 357 GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN LYS SEQRES 9 A 357 MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS LEU SEQRES 10 A 357 PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS GLU SEQRES 11 A 357 VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR ASP SEQRES 12 A 357 ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE GLU SEQRES 13 A 357 SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP GLY SEQRES 14 A 357 ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN GLU SEQRES 15 A 357 ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO VAL SEQRES 16 A 357 LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO GLN SEQRES 17 A 357 THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU PHE SEQRES 18 A 357 PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS THR SEQRES 19 A 357 ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA VAL SEQRES 20 A 357 LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR VAL SEQRES 21 A 357 VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS LYS SEQRES 22 A 357 PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU GLU SEQRES 23 A 357 ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP LEU SEQRES 24 A 357 SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL TYR SEQRES 25 A 357 ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA VAL SEQRES 26 A 357 THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU SEQRES 27 A 357 GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU SEQRES 28 A 357 ARG GLN GLU HIS HIS HIS SEQRES 1 B 357 SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN GLN SEQRES 2 B 357 GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR LEU SEQRES 3 B 357 PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET MET SEQRES 4 B 357 PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO LEU SEQRES 5 B 357 ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER ASP SEQRES 6 B 357 LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE GLY SEQRES 7 B 357 TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL GLN SEQRES 8 B 357 GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN LYS SEQRES 9 B 357 MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS LEU SEQRES 10 B 357 PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS GLU SEQRES 11 B 357 VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR ASP SEQRES 12 B 357 ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE GLU SEQRES 13 B 357 SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP GLY SEQRES 14 B 357 ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN GLU SEQRES 15 B 357 ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO VAL SEQRES 16 B 357 LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO GLN SEQRES 17 B 357 THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU PHE SEQRES 18 B 357 PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS THR SEQRES 19 B 357 ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA VAL SEQRES 20 B 357 LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR VAL SEQRES 21 B 357 VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS LYS SEQRES 22 B 357 PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU GLU SEQRES 23 B 357 ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP LEU SEQRES 24 B 357 SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL TYR SEQRES 25 B 357 ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA VAL SEQRES 26 B 357 THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU SEQRES 27 B 357 GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU SEQRES 28 B 357 ARG GLN GLU HIS HIS HIS HET SO4 A1001 5 HET GOL A1002 6 HET CQ5 A1003 34 HET SO4 B1001 5 HET SO4 B1002 5 HET CQ5 B1003 34 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM CQ5 3-[[4-OXIDANYL-1-[(3~{R})-3-PHENYLBUTANOYL]PIPERIDIN-4- HETNAM 2 CQ5 YL]METHYL]-6-(2-PYRROLIDIN-1-YLETHYLAMINO)PYRIMIDIN-4- HETNAM 3 CQ5 ONE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 GOL C3 H8 O3 FORMUL 5 CQ5 2(C26 H37 N5 O3) FORMUL 9 HOH *404(H2 O) HELIX 1 AA1 SER A 207 GLY A 212 1 6 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 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 HIS A 563 1 27 HELIX 17 AB8 TYR B 224 PHE B 234 1 11 HELIX 18 AB9 THR B 235 MET B 245 1 11 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 THR B 287 GLN B 293 1 7 HELIX 22 AC4 ASP B 295 LYS B 312 1 18 HELIX 23 AC5 GLY B 318 ARG B 325 1 8 HELIX 24 AC6 ASN B 359 VAL B 368 1 10 HELIX 25 AC7 ASP B 374 LYS B 378 5 5 HELIX 26 AC8 GLY B 382 HIS B 384 5 3 HELIX 27 AC9 ASP B 434 LEU B 437 5 4 HELIX 28 AD1 THR B 489 ILE B 494 1 6 HELIX 29 AD2 GLU B 495 TYR B 498 5 4 HELIX 30 AD3 LYS B 523 LEU B 528 1 6 HELIX 31 AD4 THR B 532 ILE B 536 5 5 HELIX 32 AD5 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 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 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 GLY B 326 O TYR B 347 SHEET 3 AA6 4 ALA B 389 THR B 397 -1 O GLY B 392 N TYR B 331 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 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 LEU B 516 N LEU B 404 SHEET 4 AA7 5 ASN B 447 SER B 457 -1 N LEU B 454 O MET B 515 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 LEU B 516 N LEU B 404 SHEET 4 AA8 7 ASN B 447 SER B 457 -1 N LEU B 454 O MET B 515 SHEET 5 AA8 7 HIS B 464 LEU B 469 -1 O TYR B 468 N VAL B 453 SHEET 6 AA8 7 CYS B 478 ASP B 481 -1 O CYS B 478 N LEU B 469 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 7 GLN A 219 ARG A 262 GLY A 275 THR A 276 SITE 2 AC1 7 LYS A 277 LYS A 278 HOH A1233 SITE 1 AC2 5 SER A 330 TYR A 331 SER A 341 LYS A 391 SITE 2 AC2 5 HOH A1140 SITE 1 AC3 15 TYR A 224 ASP A 295 VAL A 296 GLN A 297 SITE 2 AC3 15 LEU A 406 MET A 407 ARG A 408 PHE A 409 SITE 3 AC3 15 LYS A 420 HIS A 456 ASN A 460 HIS A 461 SITE 4 AC3 15 TYR A 465 TYR A 514 HOH A1159 SITE 1 AC4 8 GLY B 275 THR B 276 LYS B 277 LYS B 278 SITE 2 AC4 8 HOH B1103 HOH B1132 HOH B1154 HOH B1229 SITE 1 AC5 3 GLY B 475 THR B 489 LYS B 490 SITE 1 AC6 15 TYR B 224 ASP B 295 VAL B 296 GLN B 297 SITE 2 AC6 15 LEU B 406 MET B 407 ARG B 408 PHE B 409 SITE 3 AC6 15 LYS B 420 HIS B 456 ASN B 460 HIS B 461 SITE 4 AC6 15 TYR B 465 TYR B 514 HOH B1199 CRYST1 74.865 67.328 80.686 90.00 105.06 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 0.013357 0.000000 0.003594 0.00000 SCALE2 0.000000 0.014853 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012834 0.00000