HEADER HYDROLASE 20-DEC-18 6NFT TITLE STRUCTURE OF USP5 ZINC-FINGER UBIQUITIN BINDING DOMAIN CO-CRYSTALLIZED TITLE 2 WITH (4-OXOQUINAZOLIN-3(4H)-YL)ACETIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 5; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 5,ISOPEPTIDASE T,UBIQUITIN COMPND 5 THIOESTERASE 5,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 5; COMPND 6 EC: 3.4.19.12; COMPND 7 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: USP5, ISOT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS USP5, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.J.HARDING,M.K.MANN,W.TEMPEL,C.BOUNTRA,C.M.ARROWMSMITH,A.M.EDWARDS, AUTHOR 2 M.SCHAPIRA,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 09-JUN-21 6NFT 1 JRNL REVDAT 2 08-JAN-20 6NFT 1 REMARK REVDAT 1 02-JAN-19 6NFT 0 JRNL AUTH M.K.MANN,I.FRANZONI,R.F.DE FREITAS,W.TEMPEL,S.HOULISTON, JRNL AUTH 2 L.SMITH,M.VEDADI,C.H.ARROWSMITH,R.J.HARDING,M.SCHAPIRA JRNL TITL DISCOVERY OF SMALL MOLECULE ANTAGONISTS OF THE USP5 ZINC JRNL TITL 2 FINGER UBIQUITIN-BINDING DOMAIN. JRNL REF J.MED.CHEM. V. 62 10144 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31663737 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00988 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 34601 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1821 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2484 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 142 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1787 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 0.61000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.56000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.087 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.708 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1930 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1675 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2622 ; 1.655 ; 1.637 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3887 ; 1.502 ; 1.592 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 241 ; 7.302 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;32.955 ;22.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 296 ;11.427 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;14.968 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 233 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2341 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 408 ; 0.001 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6NFT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1000238718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36423 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 26.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.91600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M SODIUM/POTASSIUM PHOSPHATE PH 7.0, REMARK 280 1.1% DMSO (V/V), 25% ETHYLENE GLYCOL (V/V), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 30.93500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.93500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.52000 REMARK 290 SMTRY3 4 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 UNK UNX B 305 LIES ON A SPECIAL POSITION. 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 170 REMARK 465 MET A 286 REMARK 465 GLN A 287 REMARK 465 LYS A 288 REMARK 465 THR A 289 REMARK 465 ASP A 290 REMARK 465 GLY B 170 REMARK 465 GLY B 171 REMARK 465 GLU B 172 REMARK 465 ASP B 290 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 GLU A 172 CG CD OE1 OE2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 ARG A 191 CD NE CZ NH1 NH2 REMARK 470 LYS A 201 CE NZ REMARK 470 ASP A 282 CG OD1 OD2 REMARK 470 LYS A 285 CG CD CE NZ REMARK 470 VAL B 173 N CA CB CG1 CG2 REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 LYS B 201 CE NZ REMARK 470 LYS B 285 CE NZ 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 TYR A 259 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 TYR A 259 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 221 NE - CZ - NH1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 221 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 199 SG REMARK 620 2 CYS A 202 SG 113.6 REMARK 620 3 CYS A 219 SG 111.5 111.7 REMARK 620 4 HIS A 232 ND1 109.2 112.5 97.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 199 SG REMARK 620 2 CYS B 202 SG 113.8 REMARK 620 3 CYS B 219 SG 112.6 112.0 REMARK 620 4 HIS B 232 ND1 107.9 113.4 95.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KKG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KKG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6DXT RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 3-(5-PHENYL-1,3,4-OXADIAZOL-2-YL) REMARK 900 PROPANOATE REMARK 900 RELATED ID: 6DXH RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH -(4-TERT-BUTYLPHENYL)-4-OXOBUTANOATE DBREF 6NFT A 171 290 UNP P45974 UBP5_HUMAN 171 290 DBREF 6NFT B 171 290 UNP P45974 UBP5_HUMAN 171 290 SEQADV 6NFT GLY A 170 UNP P45974 EXPRESSION TAG SEQADV 6NFT GLY B 170 UNP P45974 EXPRESSION TAG SEQRES 1 A 121 GLY GLY GLU VAL ARG GLN VAL SER LYS HIS ALA PHE SER SEQRES 2 A 121 LEU LYS GLN LEU ASP ASN PRO ALA ARG ILE PRO PRO CYS SEQRES 3 A 121 GLY TRP LYS CYS SER LYS CYS ASP MET ARG GLU ASN LEU SEQRES 4 A 121 TRP LEU ASN LEU THR ASP GLY SER ILE LEU CYS GLY ARG SEQRES 5 A 121 ARG TYR PHE ASP GLY SER GLY GLY ASN ASN HIS ALA VAL SEQRES 6 A 121 GLU HIS TYR ARG GLU THR GLY TYR PRO LEU ALA VAL LYS SEQRES 7 A 121 LEU GLY THR ILE THR PRO ASP GLY ALA ASP VAL TYR SER SEQRES 8 A 121 TYR ASP GLU ASP ASP MET VAL LEU ASP PRO SER LEU ALA SEQRES 9 A 121 GLU HIS LEU SER HIS PHE GLY ILE ASP MET LEU LYS MET SEQRES 10 A 121 GLN LYS THR ASP SEQRES 1 B 121 GLY GLY GLU VAL ARG GLN VAL SER LYS HIS ALA PHE SER SEQRES 2 B 121 LEU LYS GLN LEU ASP ASN PRO ALA ARG ILE PRO PRO CYS SEQRES 3 B 121 GLY TRP LYS CYS SER LYS CYS ASP MET ARG GLU ASN LEU SEQRES 4 B 121 TRP LEU ASN LEU THR ASP GLY SER ILE LEU CYS GLY ARG SEQRES 5 B 121 ARG TYR PHE ASP GLY SER GLY GLY ASN ASN HIS ALA VAL SEQRES 6 B 121 GLU HIS TYR ARG GLU THR GLY TYR PRO LEU ALA VAL LYS SEQRES 7 B 121 LEU GLY THR ILE THR PRO ASP GLY ALA ASP VAL TYR SER SEQRES 8 B 121 TYR ASP GLU ASP ASP MET VAL LEU ASP PRO SER LEU ALA SEQRES 9 B 121 GLU HIS LEU SER HIS PHE GLY ILE ASP MET LEU LYS MET SEQRES 10 B 121 GLN LYS THR ASP HET ZN A 301 1 HET KKG A 302 15 HET EDO A 303 4 HET UNX A 304 1 HET UNX A 305 1 HET UNX A 306 1 HET UNX A 307 1 HET UNX A 308 1 HET UNX A 309 1 HET UNX A 310 1 HET UNX A 311 1 HET UNX A 312 1 HET UNX A 313 1 HET UNX A 314 1 HET ZN B 301 1 HET KKG B 302 15 HET EDO B 303 4 HET EDO B 304 4 HET UNX B 305 1 HET UNX B 306 1 HET UNX B 307 1 HET UNX B 308 1 HET UNX B 309 1 HET UNX B 310 1 HETNAM ZN ZINC ION HETNAM KKG (4-OXOQUINAZOLIN-3(4H)-YL)ACETIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM UNX UNKNOWN ATOM OR ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 KKG 2(C10 H8 N2 O3) FORMUL 5 EDO 3(C2 H6 O2) FORMUL 6 UNX 17(X) FORMUL 27 HOH *245(H2 O) HELIX 1 AA1 ASN A 231 GLY A 241 1 11 HELIX 2 AA2 SER A 271 HIS A 278 1 8 HELIX 3 AA3 ASN B 231 GLY B 241 1 11 HELIX 4 AA4 SER B 271 HIS B 278 1 8 SHEET 1 AA1 5 ILE A 217 CYS A 219 0 SHEET 2 AA1 5 LEU A 208 ASN A 211 -1 N TRP A 209 O LEU A 218 SHEET 3 AA1 5 LEU A 244 LYS A 247 -1 O VAL A 246 N LEU A 210 SHEET 4 AA1 5 VAL A 258 SER A 260 -1 O TYR A 259 N ALA A 245 SHEET 5 AA1 5 ASP A 265 VAL A 267 -1 O VAL A 267 N VAL A 258 SHEET 1 AA2 6 GLN B 175 VAL B 176 0 SHEET 2 AA2 6 ASP B 265 LEU B 268 1 O LEU B 268 N GLN B 175 SHEET 3 AA2 6 VAL B 258 SER B 260 -1 N SER B 260 O ASP B 265 SHEET 4 AA2 6 LEU B 244 LYS B 247 -1 N ALA B 245 O TYR B 259 SHEET 5 AA2 6 LEU B 208 ASN B 211 -1 N LEU B 210 O VAL B 246 SHEET 6 AA2 6 ILE B 217 CYS B 219 -1 O LEU B 218 N TRP B 209 SSBOND 1 CYS A 195 CYS B 195 1555 1555 2.20 LINK SG CYS A 199 ZN ZN A 301 1555 1555 2.33 LINK SG CYS A 202 ZN ZN A 301 1555 1555 2.30 LINK SG CYS A 219 ZN ZN A 301 1555 1555 2.32 LINK ND1 HIS A 232 ZN ZN A 301 1555 1555 2.04 LINK SG CYS B 199 ZN ZN B 301 1555 1555 2.29 LINK SG CYS B 202 ZN ZN B 301 1555 1555 2.31 LINK SG CYS B 219 ZN ZN B 301 1555 1555 2.32 LINK ND1 HIS B 232 ZN ZN B 301 1555 1555 2.09 SITE 1 AC1 4 CYS A 199 CYS A 202 CYS A 219 HIS A 232 SITE 1 AC2 10 TRP A 209 GLY A 220 ARG A 221 TYR A 223 SITE 2 AC2 10 TYR A 259 TYR A 261 MET A 266 HOH A 435 SITE 3 AC2 10 HOH A 444 HOH A 482 SITE 1 AC3 4 VAL A 176 GLU A 263 VAL A 267 HOH A 440 SITE 1 AC4 4 CYS B 199 CYS B 202 CYS B 219 HIS B 232 SITE 1 AC5 10 TRP B 209 GLY B 220 ARG B 221 TYR B 223 SITE 2 AC5 10 ALA B 233 TYR B 259 TYR B 261 HOH B 425 SITE 3 AC5 10 HOH B 432 HOH B 458 SITE 1 AC6 7 HOH A 422 LEU B 186 ASP B 187 ASN B 188 SITE 2 AC6 7 PRO B 189 ASP B 214 HOH B 465 SITE 1 AC7 5 GLN B 175 VAL B 176 GLU B 263 ASP B 265 SITE 2 AC7 5 HOH B 442 CRYST1 61.870 85.040 59.840 90.00 99.00 90.00 C 1 2 1 8 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 0.016163 0.000000 0.002560 0.00000 SCALE2 0.000000 0.011759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016920 0.00000