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 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 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 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