HEADER HYDROLASE 29-JAN-20 6VN6
TITLE USP7 IN COMPLEX WITH LIGAND COMPOUND 14
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 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606
KEYWDS USP7, DUB, DEUBIQUITINASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR P.R.LEGER,D.J.WUSTROW,D.X.HU,S.KRAPP,K.MASKOS,M.BLAESSE
REVDAT 4 13-NOV-24 6VN6 1 REMARK
REVDAT 3 03-APR-24 6VN6 1 REMARK
REVDAT 2 10-JUN-20 6VN6 1 JRNL
REVDAT 1 29-APR-20 6VN6 0
JRNL AUTH P.R.LEGER,D.X.HU,B.BIANNIC,M.BUI,X.HAN,E.KARBARZ,J.MAUNG,
JRNL AUTH 2 A.OKANO,M.OSIPOV,G.M.SHIBUYA,K.YOUNG,C.HIGGS,B.ABRAHAM,
JRNL AUTH 3 D.BRADFORD,C.CHO,C.COLAS,S.JACOBSON,Y.M.OHOL,D.POOKOT,
JRNL AUTH 4 P.RANA,J.SANCHEZ,N.SHAH,M.SUN,S.WONG,D.G.BROCKSTEDT,
JRNL AUTH 5 P.D.KASSNER,J.B.SCHWARZ,D.J.WUSTROW
JRNL TITL DISCOVERY OF POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE
JRNL TITL 2 INHIBITORS OF USP7 WITH IN VIVO ANTITUMOR ACTIVITY.
JRNL REF J.MED.CHEM. V. 63 5398 2020
JRNL REFN ISSN 0022-2623
JRNL PMID 32302140
JRNL DOI 10.1021/ACS.JMEDCHEM.0C00245
REMARK 2
REMARK 2 RESOLUTION. 2.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0155
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) : 2.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.90
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 3 NUMBER OF REFLECTIONS : 14845
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) : 0.221
REMARK 3 R VALUE (WORKING SET) : 0.219
REMARK 3 FREE R VALUE : 0.267
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.800
REMARK 3 FREE R VALUE TEST SET COUNT : 590
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) : 2.99
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.07
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1088
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.77
REMARK 3 BIN R VALUE (WORKING SET) : 0.3220
REMARK 3 BIN FREE R VALUE SET COUNT : 51
REMARK 3 BIN FREE R VALUE : 0.4140
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5470
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 68
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 72.36
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 99.58
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -4.44000
REMARK 3 B22 (A**2) : 1.48000
REMARK 3 B33 (A**2) : 2.42000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 3.62000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.492
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.444
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 54.622
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5514 ; 0.010 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 5131 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7463 ; 1.355 ; 1.978
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11804 ; 1.145 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 667 ; 6.603 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 267 ;37.771 ;24.944
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 947 ;12.775 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;10.488 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 808 ; 0.076 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6251 ; 0.005 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1243 ; 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 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 207 553 B 207 553 20178 0.070 0.050
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): 20.742 1.130 40.884
REMARK 3 T TENSOR
REMARK 3 T11: 0.0769 T22: 0.1427
REMARK 3 T33: 0.0512 T12: 0.0321
REMARK 3 T13: 0.0273 T23: 0.0428
REMARK 3 L TENSOR
REMARK 3 L11: 5.6951 L22: 3.0447
REMARK 3 L33: 2.0409 L12: -0.0271
REMARK 3 L13: 0.2755 L23: 0.4133
REMARK 3 S TENSOR
REMARK 3 S11: 0.1111 S12: 0.6901 S13: -0.0688
REMARK 3 S21: -0.2039 S22: -0.0283 S23: -0.1538
REMARK 3 S31: -0.3647 S32: -0.0118 S33: -0.0829
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 553
REMARK 3 ORIGIN FOR THE GROUP (A): 3.408 4.792 79.667
REMARK 3 T TENSOR
REMARK 3 T11: 0.2410 T22: 0.1659
REMARK 3 T33: 0.1233 T12: -0.0353
REMARK 3 T13: 0.0210 T23: 0.0027
REMARK 3 L TENSOR
REMARK 3 L11: 5.1276 L22: 2.4703
REMARK 3 L33: 2.6459 L12: -0.2769
REMARK 3 L13: -2.0494 L23: -0.0779
REMARK 3 S TENSOR
REMARK 3 S11: 0.0251 S12: -0.5906 S13: -0.0250
REMARK 3 S21: 0.4903 S22: -0.0876 S23: 0.2571
REMARK 3 S31: -0.1248 S32: 0.2434 S33: 0.0625
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: U VALUES : WITH TLS ADDED HYDROGENS
REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS
REMARK 4
REMARK 4 6VN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JAN-20.
REMARK 100 THE DEPOSITION ID IS D_1000246511.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-NOV-16
REMARK 200 TEMPERATURE (KELVIN) : 100.000
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X06SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.00
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15436
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990
REMARK 200 RESOLUTION RANGE LOW (A) : 85.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 200 DATA REDUNDANCY : 2.650
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.99
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.24
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.70
REMARK 200 R MERGE FOR SHELL (I) : 0.43700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.390
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: INHOUSE MODEL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL, VAPOR DIFFUSION, TEMPERATURE
REMARK 280 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 32.84000
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 GLN A 219
REMARK 465 GLY A 220
REMARK 465 ALA A 221
REMARK 465 GLY A 500
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 A 509
REMARK 465 CYS A 510
REMARK 465 GLY B 206
REMARK 465 GLY B 500
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 465 HIS B 509
REMARK 465 LYS B 554
REMARK 465 ARG B 555
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 LEU A 288 CG CD1 CD2
REMARK 480 GLN A 293 CD OE1 NE2
REMARK 480 ARG A 301 CD NE CZ NH1 NH2
REMARK 480 LYS A 335 CE NZ
REMARK 480 LYS A 358 CG CD CE NZ
REMARK 480 LYS A 378 CG CD CE NZ
REMARK 480 GLU A 383 CD OE1 OE2
REMARK 480 GLU A 388 CG CD OE1 OE2
REMARK 480 LYS A 394 CG CD CE NZ
REMARK 480 TYR A 411 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 480 GLN A 414 CG CD OE1 NE2
REMARK 480 ASP A 416 CG OD1 OD2
REMARK 480 GLN A 417 CD OE1 NE2
REMARK 480 GLN A 438 CD OE1 NE2
REMARK 480 LYS A 439 CG CD CE NZ
REMARK 480 HIS A 461 CG ND1 CD2 CE1 NE2
REMARK 480 HIS A 464 CG ND1 CD2 CE1 NE2
REMARK 480 LEU B 288 CG CD1 CD2
REMARK 480 ASP B 289 CG OD1 OD2
REMARK 480 MET B 292 CE
REMARK 480 GLN B 293 CG CD OE1 NE2
REMARK 480 LYS B 335 CG CD CE NZ
REMARK 480 LYS B 355 CG CD CE NZ
REMARK 480 LYS B 357 CD CE NZ
REMARK 480 LYS B 358 CG CD CE NZ
REMARK 480 LYS B 378 CG CD CE NZ
REMARK 480 GLU B 388 CG CD OE1 OE2
REMARK 480 GLU B 390 CG CD OE1 OE2
REMARK 480 LYS B 391 CG CD CE NZ
REMARK 480 LYS B 394 CG CD CE NZ
REMARK 480 MET B 410 CE
REMARK 480 TYR B 411 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 480 GLN B 414 CG CD OE1 NE2
REMARK 480 THR B 415 OG1 CG2
REMARK 480 ASP B 416 CG OD1 OD2
REMARK 480 GLN B 417 CG CD OE1 NE2
REMARK 480 ASN B 418 CG OD1 ND2
REMARK 480 LYS B 439 CG CD CE NZ
REMARK 480 HIS B 461 CG ND1 CD2 CE1 NE2
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 -72.63 -74.18
REMARK 500 ASP A 482 -104.93 49.55
REMARK 500 ILE A 494 -76.77 -81.59
REMARK 500 ASN A 497 50.02 -97.22
REMARK 500 TYR A 498 -64.20 -107.33
REMARK 500 LEU A 528 33.55 -98.56
REMARK 500 LYS A 554 44.46 -153.07
REMARK 500 THR B 222 84.16 -68.40
REMARK 500 CYS B 223 -72.87 -73.15
REMARK 500 ASP B 412 72.95 67.01
REMARK 500 PRO B 413 74.53 -100.03
REMARK 500 THR B 415 -147.89 -119.92
REMARK 500 ASP B 416 39.45 -152.67
REMARK 500 ASP B 482 -104.94 49.31
REMARK 500 ILE B 494 -76.64 -82.14
REMARK 500 ASN B 497 49.99 -97.52
REMARK 500 TYR B 498 -64.45 -107.02
REMARK 500 LEU B 528 33.82 -98.76
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 602 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 300 SG
REMARK 620 2 ASP A 349 OD1 137.2
REMARK 620 3 HIS A 403 ND1 112.3 110.0
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 602 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 300 SG
REMARK 620 2 ASP B 349 OD1 136.1
REMARK 620 3 HIS B 403 ND1 111.9 110.3
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue R4J A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue R4J B 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 602
DBREF 6VN6 A 207 555 UNP Q93009 UBP7_HUMAN 207 555
DBREF 6VN6 B 207 555 UNP Q93009 UBP7_HUMAN 207 555
SEQADV 6VN6 GLY A 206 UNP Q93009 EXPRESSION TAG
SEQADV 6VN6 GLY B 206 UNP Q93009 EXPRESSION TAG
SEQRES 1 A 350 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN
SEQRES 2 A 350 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR
SEQRES 3 A 350 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET
SEQRES 4 A 350 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO
SEQRES 5 A 350 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER
SEQRES 6 A 350 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE
SEQRES 7 A 350 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL
SEQRES 8 A 350 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN
SEQRES 9 A 350 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS
SEQRES 10 A 350 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS
SEQRES 11 A 350 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR
SEQRES 12 A 350 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE
SEQRES 13 A 350 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP
SEQRES 14 A 350 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN
SEQRES 15 A 350 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO
SEQRES 16 A 350 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO
SEQRES 17 A 350 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU
SEQRES 18 A 350 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS
SEQRES 19 A 350 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA
SEQRES 20 A 350 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR
SEQRES 21 A 350 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS
SEQRES 22 A 350 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU
SEQRES 23 A 350 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP
SEQRES 24 A 350 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL
SEQRES 25 A 350 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA
SEQRES 26 A 350 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG
SEQRES 27 A 350 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG
SEQRES 1 B 350 GLY SER LYS LYS HIS THR GLY TYR VAL GLY LEU LYS ASN
SEQRES 2 B 350 GLN GLY ALA THR CYS TYR MET ASN SER LEU LEU GLN THR
SEQRES 3 B 350 LEU PHE PHE THR ASN GLN LEU ARG LYS ALA VAL TYR MET
SEQRES 4 B 350 MET PRO THR GLU GLY ASP ASP SER SER LYS SER VAL PRO
SEQRES 5 B 350 LEU ALA LEU GLN ARG VAL PHE TYR GLU LEU GLN HIS SER
SEQRES 6 B 350 ASP LYS PRO VAL GLY THR LYS LYS LEU THR LYS SER PHE
SEQRES 7 B 350 GLY TRP GLU THR LEU ASP SER PHE MET GLN HIS ASP VAL
SEQRES 8 B 350 GLN GLU LEU CYS ARG VAL LEU LEU ASP ASN VAL GLU ASN
SEQRES 9 B 350 LYS MET LYS GLY THR CYS VAL GLU GLY THR ILE PRO LYS
SEQRES 10 B 350 LEU PHE ARG GLY LYS MET VAL SER TYR ILE GLN CYS LYS
SEQRES 11 B 350 GLU VAL ASP TYR ARG SER ASP ARG ARG GLU ASP TYR TYR
SEQRES 12 B 350 ASP ILE GLN LEU SER ILE LYS GLY LYS LYS ASN ILE PHE
SEQRES 13 B 350 GLU SER PHE VAL ASP TYR VAL ALA VAL GLU GLN LEU ASP
SEQRES 14 B 350 GLY ASP ASN LYS TYR ASP ALA GLY GLU HIS GLY LEU GLN
SEQRES 15 B 350 GLU ALA GLU LYS GLY VAL LYS PHE LEU THR LEU PRO PRO
SEQRES 16 B 350 VAL LEU HIS LEU GLN LEU MET ARG PHE MET TYR ASP PRO
SEQRES 17 B 350 GLN THR ASP GLN ASN ILE LYS ILE ASN ASP ARG PHE GLU
SEQRES 18 B 350 PHE PRO GLU GLN LEU PRO LEU ASP GLU PHE LEU GLN LYS
SEQRES 19 B 350 THR ASP PRO LYS ASP PRO ALA ASN TYR ILE LEU HIS ALA
SEQRES 20 B 350 VAL LEU VAL HIS SER GLY ASP ASN HIS GLY GLY HIS TYR
SEQRES 21 B 350 VAL VAL TYR LEU ASN PRO LYS GLY ASP GLY LYS TRP CYS
SEQRES 22 B 350 LYS PHE ASP ASP ASP VAL VAL SER ARG CYS THR LYS GLU
SEQRES 23 B 350 GLU ALA ILE GLU HIS ASN TYR GLY GLY HIS ASP ASP ASP
SEQRES 24 B 350 LEU SER VAL ARG HIS CYS THR ASN ALA TYR MET LEU VAL
SEQRES 25 B 350 TYR ILE ARG GLU SER LYS LEU SER GLU VAL LEU GLN ALA
SEQRES 26 B 350 VAL THR ASP HIS ASP ILE PRO GLN GLN LEU VAL GLU ARG
SEQRES 27 B 350 LEU GLN GLU GLU LYS ARG ILE GLU ALA GLN LYS ARG
HET R4J A 601 33
HET ZN A 602 1
HET R4J B 601 33
HET ZN B 602 1
HETNAM R4J [(2R)-5-CHLORO-7-{2-[(2S)-1-CHLORO-2,3-DIHYDROXYPROPAN-
HETNAM 2 R4J 2-YL]THIENO[3,2-B]PYRIDIN-7-YL}-2,3-DIHYDRO-1-
HETNAM 3 R4J BENZOFURAN-2-YL](PIPERAZIN-1-YL)METHANONE
HETNAM ZN ZINC ION
FORMUL 3 R4J 2(C23 H23 CL2 N3 O4 S)
FORMUL 4 ZN 2(ZN 2+)
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 PHE A 283 1 8
HELIX 6 AA6 THR A 287 HIS A 294 1 8
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 VAL A 368 1 10
HELIX 10 AB1 PRO A 413 ASP A 416 5 4
HELIX 11 AB2 THR A 489 ILE A 494 1 6
HELIX 12 AB3 LYS A 523 LEU A 528 1 6
HELIX 13 AB4 THR A 532 ILE A 536 5 5
HELIX 14 AB5 PRO A 537 GLN A 553 1 17
HELIX 15 AB6 LYS B 208 GLY B 212 1 5
HELIX 16 AB7 TYR B 224 PHE B 234 1 11
HELIX 17 AB8 THR B 235 MET B 244 1 10
HELIX 18 AB9 SER B 255 SER B 270 1 16
HELIX 19 AC1 THR B 276 PHE B 283 1 8
HELIX 20 AC2 THR B 287 HIS B 294 1 8
HELIX 21 AC3 ASP B 295 LYS B 312 1 18
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 434 LEU B 437 5 4
HELIX 25 AC7 THR B 489 ILE B 494 1 6
HELIX 26 AC8 LYS B 523 LEU B 528 1 6
HELIX 27 AC9 THR B 532 ILE B 536 5 5
HELIX 28 AD1 PRO B 537 GLN B 553 1 17
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 GLU A 371 O LYS A 391
SHEET 1 AA2 5 ASP A 349 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 ILE A 449 O ILE A 519
SHEET 5 AA2 5 GLN A 430 PRO A 432 -1 N LEU A 431 O TYR A 448
SHEET 1 AA3 7 ASP A 349 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 ILE A 449 O ILE A 519
SHEET 5 AA3 7 HIS A 464 LEU A 469 -1 O TYR A 468 N VAL A 453
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 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 GLU B 390 N GLN B 333
SHEET 4 AA6 4 GLU B 371 LEU B 373 -1 N GLU B 371 O LYS B 391
SHEET 1 AA7 5 ASP B 349 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 TYR B 518 N LEU B 402
SHEET 4 AA7 5 ASN B 447 SER B 457 -1 N ILE B 449 O ILE B 519
SHEET 5 AA7 5 GLN B 430 PRO B 432 -1 N LEU B 431 O TYR B 448
SHEET 1 AA8 7 ASP B 349 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 TYR B 518 N LEU B 402
SHEET 4 AA8 7 ASN B 447 SER B 457 -1 N ILE B 449 O ILE B 519
SHEET 5 AA8 7 HIS B 464 LEU B 469 -1 O TYR B 468 N VAL B 453
SHEET 6 AA8 7 TRP B 477 ASP B 481 -1 O PHE B 480 N VAL B 467
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 PHE B 409 TYR B 411 0
SHEET 2 AB1 2 ASN B 418 LYS B 420 -1 O ILE B 419 N MET B 410
SSBOND 1 CYS A 315 CYS B 315 1555 1555 2.04
LINK SG CYS A 300 ZN ZN A 602 1555 1555 2.34
LINK OD1 ASP A 349 ZN ZN A 602 1555 1555 1.99
LINK ND1 HIS A 403 ZN ZN A 602 1555 1555 2.07
LINK SG CYS B 300 ZN ZN B 602 1555 1555 2.35
LINK OD1 ASP B 349 ZN ZN B 602 1555 1555 1.99
LINK ND1 HIS B 403 ZN ZN B 602 1555 1555 2.07
SITE 1 AC1 15 TYR A 224 MET A 292 HIS A 294 ASP A 295
SITE 2 AC1 15 VAL A 296 GLN A 297 GLN A 351 GLN A 405
SITE 3 AC1 15 LEU A 406 MET A 407 ARG A 408 PHE A 409
SITE 4 AC1 15 HIS A 456 ASN A 460 TYR A 465
SITE 1 AC2 3 CYS A 300 ASP A 349 HIS A 403
SITE 1 AC3 14 MET B 292 HIS B 294 ASP B 295 VAL B 296
SITE 2 AC3 14 GLN B 297 GLN B 351 GLN B 405 LEU B 406
SITE 3 AC3 14 MET B 407 ARG B 408 PHE B 409 HIS B 456
SITE 4 AC3 14 TYR B 465 TYR B 514
SITE 1 AC4 3 CYS B 300 ASP B 349 HIS B 403
CRYST1 70.301 65.680 85.313 90.00 94.04 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 0.014225 0.000000 0.001004 0.00000
SCALE2 0.000000 0.015225 0.000000 0.00000
SCALE3 0.000000 0.000000 0.011751 0.00000