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 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 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