HEADER HYDROLASE 29-JAN-20 6VN4
TITLE USP7 IN COMPLEX WITH LIGAND COMPOUND 1
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, 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 23-OCT-24 6VN4 1 REMARK
REVDAT 3 03-APR-24 6VN4 1 REMARK
REVDAT 2 10-JUN-20 6VN4 1 JRNL
REVDAT 1 29-APR-20 6VN4 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. 2.69 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
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) : 2.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5
REMARK 3 NUMBER OF REFLECTIONS : 21120
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) : 0.244
REMARK 3 R VALUE (WORKING SET) : 0.242
REMARK 3 FREE R VALUE : 0.300
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.300
REMARK 3 FREE R VALUE TEST SET COUNT : 724
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) : 2.69
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1573
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.08
REMARK 3 BIN R VALUE (WORKING SET) : 0.5570
REMARK 3 BIN FREE R VALUE SET COUNT : 54
REMARK 3 BIN FREE R VALUE : 0.6430
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5541
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 60
REMARK 3 SOLVENT ATOMS : 25
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 75.08
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.73
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.21000
REMARK 3 B22 (A**2) : -1.16000
REMARK 3 B33 (A**2) : 1.29000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.57000
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): 0.419
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.374
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.614
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5462 ; 0.015 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 5007 ; 0.005 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7421 ; 1.731 ; 1.965
REMARK 3 BOND ANGLES OTHERS (DEGREES): 11454 ; 1.311 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 681 ; 7.081 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 252 ;42.013 ;24.841
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 862 ;15.199 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.666 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 816 ; 0.092 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6289 ; 0.007 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1265 ; 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): 81.886 -0.610 78.842
REMARK 3 T TENSOR
REMARK 3 T11: 0.0263 T22: 0.1514
REMARK 3 T33: 0.1371 T12: -0.0207
REMARK 3 T13: -0.0390 T23: -0.0433
REMARK 3 L TENSOR
REMARK 3 L11: 3.8698 L22: 3.6827
REMARK 3 L33: 1.9259 L12: -0.5146
REMARK 3 L13: -0.1941 L23: -0.3968
REMARK 3 S TENSOR
REMARK 3 S11: 0.0733 S12: 0.0061 S13: 0.2220
REMARK 3 S21: -0.0429 S22: 0.0059 S23: 0.1261
REMARK 3 S31: 0.0018 S32: 0.0477 S33: -0.0791
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 206 B 555
REMARK 3 ORIGIN FOR THE GROUP (A): 94.995 -0.768 117.771
REMARK 3 T TENSOR
REMARK 3 T11: 0.0334 T22: 0.1481
REMARK 3 T33: 0.1352 T12: 0.0191
REMARK 3 T13: -0.0448 T23: 0.0413
REMARK 3 L TENSOR
REMARK 3 L11: 4.0879 L22: 3.8831
REMARK 3 L33: 1.9865 L12: 0.5452
REMARK 3 L13: -0.3065 L23: 0.4750
REMARK 3 S TENSOR
REMARK 3 S11: 0.0843 S12: -0.0912 S13: 0.2171
REMARK 3 S21: 0.1131 S22: -0.0008 S23: -0.1426
REMARK 3 S31: 0.0157 S32: -0.0481 S33: -0.0834
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 6VN4 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_1000246556.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 14-MAY-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 : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999
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 : 21844
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690
REMARK 200 RESOLUTION RANGE LOW (A) : 78.410
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4
REMARK 200 DATA REDUNDANCY : 3.000
REMARK 200 R MERGE (I) : 0.03700
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.8600
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.00
REMARK 200 R MERGE FOR SHELL (I) : 0.44900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.720
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: IN HOUSE MODEL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.81
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66
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 35.35750
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 HIS A 501
REMARK 465 ASP A 502
REMARK 465 ASP A 503
REMARK 465 ASP A 504
REMARK 465 LEU A 505
REMARK 465 SER A 506
REMARK 465 VAL A 507
REMARK 465 ARG A 508
REMARK 465 HIS B 501
REMARK 465 ASP B 502
REMARK 465 ASP B 503
REMARK 465 ASP B 504
REMARK 465 LEU B 505
REMARK 465 SER B 506
REMARK 465 VAL B 507
REMARK 465 ARG B 508
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ARG A 343 CG CD NE
REMARK 470 ARG B 343 CD NE
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 LYS A 209 CG CD CE NZ
REMARK 480 LYS A 217 NZ
REMARK 480 LYS A 254 CD CE NZ
REMARK 480 LYS A 272 CG CD CE NZ
REMARK 480 LYS A 277 NZ
REMARK 480 LYS A 278 CE NZ
REMARK 480 LYS A 281 CD CE NZ
REMARK 480 LYS A 322 CD CE NZ
REMARK 480 ARG A 325 CG CD NE CZ NH1 NH2
REMARK 480 LYS A 327 CE NZ
REMARK 480 LYS A 335 CG CD CE NZ
REMARK 480 GLU A 336 CD OE1 OE2
REMARK 480 VAL A 337 CG1 CG2
REMARK 480 ARG A 343 CZ NH1 NH2
REMARK 480 ARG A 344 CG CD NE CZ NH1 NH2
REMARK 480 LYS A 358 CG CD CE NZ
REMARK 480 ASP A 374 CG OD1 OD2
REMARK 480 ASP A 376 CG OD1 OD2
REMARK 480 ASN A 377 CG OD1 ND2
REMARK 480 LYS A 378 CD CE NZ
REMARK 480 LEU A 386 CG CD1 CD2
REMARK 480 GLU A 388 CG CD OE1 OE2
REMARK 480 GLU A 390 CG CD OE1 OE2
REMARK 480 LYS A 394 CG CD CE NZ
REMARK 480 GLN A 414 CG CD OE1 NE2
REMARK 480 GLN A 417 CG CD OE1 NE2
REMARK 480 LYS A 439 CD CE NZ
REMARK 480 LYS A 443 CG CD CE NZ
REMARK 480 LYS A 472 CE NZ
REMARK 480 LYS A 476 CG CD CE NZ
REMARK 480 GLU A 492 CG CD OE1 OE2
REMARK 480 LYS A 523 NZ
REMARK 480 GLN A 538 CD OE1 NE2
REMARK 480 GLN A 539 CG CD OE1 NE2
REMARK 480 GLU A 542 CG CD OE1 OE2
REMARK 480 GLN A 545 CD OE1 NE2
REMARK 480 GLU A 546 CD OE1 OE2
REMARK 480 LYS A 548 CE NZ
REMARK 480 GLU A 551 CG CD OE1 OE2
REMARK 480 GLN A 553 CD OE1 NE2
REMARK 480 LYS A 554 CG CD CE NZ
REMARK 480 ARG A 555 CG CD NE CZ NH1 NH2
REMARK 480 LYS B 209 CG CD CE NZ
REMARK 480 LYS B 254 CD CE NZ
REMARK 480 LYS B 272 CG CD CE NZ
REMARK 480 LYS B 277 CE NZ
REMARK 480 LYS B 278 CE NZ
REMARK 480 LYS B 281 CD CE NZ
REMARK 480 LYS B 322 CD CE NZ
REMARK 480 ARG B 325 CD NE CZ NH1 NH2
REMARK 480 LYS B 327 CE NZ
REMARK 480 LYS B 335 CG CD CE NZ
REMARK 480 GLU B 336 CG CD OE1 OE2
REMARK 480 ARG B 343 CZ NH1 NH2
REMARK 480 ARG B 344 CG CD NE CZ NH1 NH2
REMARK 480 LYS B 355 NZ
REMARK 480 LYS B 358 CG CD CE NZ
REMARK 480 ASP B 374 CG OD1 OD2
REMARK 480 ASP B 376 CG OD1 OD2
REMARK 480 ASN B 377 CG OD1 ND2
REMARK 480 LYS B 378 CE NZ
REMARK 480 GLU B 383 CD OE1 OE2
REMARK 480 LEU B 386 CG CD1 CD2
REMARK 480 GLU B 388 CG CD OE1 OE2
REMARK 480 GLU B 390 CG CD OE1 OE2
REMARK 480 LYS B 394 CG CD CE NZ
REMARK 480 GLN B 414 CG CD OE1 NE2
REMARK 480 GLN B 417 CG CD OE1 NE2
REMARK 480 LYS B 439 CD CE NZ
REMARK 480 LYS B 443 CG CD CE NZ
REMARK 480 LYS B 472 CE NZ
REMARK 480 LYS B 476 CG CD CE NZ
REMARK 480 GLU B 492 CG CD OE1 OE2
REMARK 480 GLN B 538 CD OE1 NE2
REMARK 480 GLN B 539 CD OE1 NE2
REMARK 480 GLU B 542 CG CD OE1 OE2
REMARK 480 GLN B 545 CD OE1 NE2
REMARK 480 GLU B 546 CD OE1 OE2
REMARK 480 GLU B 551 CG CD OE1 OE2
REMARK 480 GLN B 553 CD OE1 NE2
REMARK 480 LYS B 554 CG CD CE NZ
REMARK 480 ARG B 555 CG CD NE CZ NH1 NH2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 ARG A 262 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 CYS A 223 -102.12 61.89
REMARK 500 THR A 247 54.71 -92.91
REMARK 500 TRP A 285 63.84 -107.26
REMARK 500 GLU A 336 -70.85 -67.90
REMARK 500 LYS A 355 108.22 -56.29
REMARK 500 ALA A 446 59.74 -95.41
REMARK 500 HIS A 464 110.76 -167.23
REMARK 500 ASP A 481 76.68 -115.71
REMARK 500 ASP A 482 -112.32 56.71
REMARK 500 ILE A 494 -91.77 -97.13
REMARK 500 SER B 207 -48.68 -164.53
REMARK 500 CYS B 223 -102.63 61.46
REMARK 500 THR B 247 54.64 -93.31
REMARK 500 TRP B 285 64.12 -107.97
REMARK 500 ASP B 376 -66.78 -103.42
REMARK 500 ALA B 446 59.71 -92.94
REMARK 500 HIS B 464 110.28 -169.58
REMARK 500 ASP B 481 72.82 -116.74
REMARK 500 ASP B 482 -112.55 58.80
REMARK 500 ILE B 494 -91.20 -98.83
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 R4D A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue R4D B 601
DBREF 6VN4 A 207 555 UNP Q93009 UBP7_HUMAN 207 555
DBREF 6VN4 B 207 555 UNP Q93009 UBP7_HUMAN 207 555
SEQADV 6VN4 GLY A 206 UNP Q93009 EXPRESSION TAG
SEQADV 6VN4 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 R4D A 601 30
HET R4D B 601 30
HETNAM R4D 3-({4-HYDROXY-1-[(2R)-2-METHYL-3-
HETNAM 2 R4D PHENYLPROPANOYL]PIPERIDIN-4-YL}METHYL)QUINAZOLIN-
HETNAM 3 R4D 4(3H)-ONE
FORMUL 3 R4D 2(C24 H27 N3 O3)
FORMUL 5 HOH *25(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 ASP A 289 HIS A 294 1 6
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 ALA A 369 1 11
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 ARG A 555 1 19
HELIX 17 AB8 SER B 207 GLY B 212 1 6
HELIX 18 AB9 TYR B 224 PHE B 234 1 11
HELIX 19 AC1 THR B 235 MET B 244 1 10
HELIX 20 AC2 SER B 255 SER B 270 1 16
HELIX 21 AC3 THR B 276 GLY B 284 1 9
HELIX 22 AC4 ASP B 289 HIS B 294 1 6
HELIX 23 AC5 ASP B 295 MET B 311 1 17
HELIX 24 AC6 GLY B 318 ARG B 325 1 8
HELIX 25 AC7 ASN B 359 ALA B 369 1 11
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 ARG B 555 1 19
SHEET 1 AA1 3 ARG A 344 TYR A 347 0
SHEET 2 AA1 3 GLY A 326 VAL A 329 -1 N MET A 328 O GLU A 345
SHEET 3 AA1 3 LYS A 394 THR A 397 -1 O LEU A 396 N LYS A 327
SHEET 1 AA2 4 ARG A 340 SER A 341 0
SHEET 2 AA2 4 ILE A 332 CYS A 334 -1 N ILE A 332 O SER A 341
SHEET 3 AA2 4 ALA A 389 LYS A 391 -1 O GLU A 390 N GLN A 333
SHEET 4 AA2 4 GLU A 371 LEU A 373 -1 N GLU A 371 O LYS A 391
SHEET 1 AA3 5 ILE A 350 SER A 353 0
SHEET 2 AA3 5 VAL A 401 MET A 407 1 O MET A 407 N LEU A 352
SHEET 3 AA3 5 ASN A 512 ARG A 520 -1 O TYR A 514 N LEU A 406
SHEET 4 AA3 5 ASN A 447 SER A 457 -1 N ILE A 449 O ILE A 519
SHEET 5 AA3 5 GLN A 430 PRO A 432 -1 N LEU A 431 O TYR A 448
SHEET 1 AA4 7 ILE A 350 SER A 353 0
SHEET 2 AA4 7 VAL A 401 MET A 407 1 O MET A 407 N LEU A 352
SHEET 3 AA4 7 ASN A 512 ARG A 520 -1 O TYR A 514 N LEU A 406
SHEET 4 AA4 7 ASN A 447 SER A 457 -1 N ILE A 449 O ILE A 519
SHEET 5 AA4 7 HIS A 464 LEU A 469 -1 O VAL A 466 N VAL A 455
SHEET 6 AA4 7 CYS A 478 ASP A 481 -1 O PHE A 480 N VAL A 467
SHEET 7 AA4 7 VAL A 484 ARG A 487 -1 O VAL A 484 N ASP A 481
SHEET 1 AA5 2 TYR A 379 ASP A 380 0
SHEET 2 AA5 2 LEU A 386 GLN A 387 -1 O GLN A 387 N TYR A 379
SHEET 1 AA6 2 PHE A 409 ASP A 412 0
SHEET 2 AA6 2 GLN A 417 LYS A 420 -1 O ILE A 419 N MET A 410
SHEET 1 AA7 3 ARG B 344 TYR B 347 0
SHEET 2 AA7 3 GLY B 326 VAL B 329 -1 N GLY B 326 O TYR B 347
SHEET 3 AA7 3 LYS B 394 THR B 397 -1 O LEU B 396 N LYS B 327
SHEET 1 AA8 4 ARG B 340 SER B 341 0
SHEET 2 AA8 4 ILE B 332 CYS B 334 -1 N ILE B 332 O SER B 341
SHEET 3 AA8 4 ALA B 389 LYS B 391 -1 O GLU B 390 N GLN B 333
SHEET 4 AA8 4 GLU B 371 LEU B 373 -1 N GLU B 371 O LYS B 391
SHEET 1 AA9 5 ILE B 350 SER B 353 0
SHEET 2 AA9 5 VAL B 401 MET B 407 1 O MET B 407 N LEU B 352
SHEET 3 AA9 5 ASN B 512 ARG B 520 -1 O TYR B 514 N LEU B 406
SHEET 4 AA9 5 ASN B 447 SER B 457 -1 N ILE B 449 O ILE B 519
SHEET 5 AA9 5 GLN B 430 PRO B 432 -1 N LEU B 431 O TYR B 448
SHEET 1 AB1 7 ILE B 350 SER B 353 0
SHEET 2 AB1 7 VAL B 401 MET B 407 1 O MET B 407 N LEU B 352
SHEET 3 AB1 7 ASN B 512 ARG B 520 -1 O TYR B 514 N LEU B 406
SHEET 4 AB1 7 ASN B 447 SER B 457 -1 N ILE B 449 O ILE B 519
SHEET 5 AB1 7 HIS B 464 LEU B 469 -1 O VAL B 466 N VAL B 455
SHEET 6 AB1 7 CYS B 478 ASP B 481 -1 O PHE B 480 N VAL B 467
SHEET 7 AB1 7 VAL B 484 ARG B 487 -1 O VAL B 484 N ASP B 481
SHEET 1 AB2 2 TYR B 379 ASP B 380 0
SHEET 2 AB2 2 LEU B 386 GLN B 387 -1 O GLN B 387 N TYR B 379
SHEET 1 AB3 2 PHE B 409 ASP B 412 0
SHEET 2 AB3 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 2.07
SITE 1 AC1 15 TYR A 224 MET A 292 ASP A 295 VAL A 296
SITE 2 AC1 15 GLN A 297 GLN A 405 LEU A 406 MET A 407
SITE 3 AC1 15 ARG A 408 PHE A 409 LYS A 420 HIS A 456
SITE 4 AC1 15 HIS A 461 TYR A 465 TYR A 514
SITE 1 AC2 14 TYR B 224 ASP B 295 VAL B 296 GLN B 297
SITE 2 AC2 14 GLN B 405 LEU B 406 MET B 407 ARG B 408
SITE 3 AC2 14 PHE B 409 LYS B 420 HIS B 456 HIS B 461
SITE 4 AC2 14 TYR B 465 TYR B 514
CRYST1 75.380 70.715 78.551 90.00 93.40 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 0.013266 0.000000 0.000789 0.00000
SCALE2 0.000000 0.014141 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012753 0.00000