PDB Short entry for 5XU8 HEADER HYDROLASE 22-JUN-17 5XU8 TITLE CRYSTAL STRUCTURE OF HUMAN USP2 IN COMPLEX WITH UBIQUITIN AND 6- TITLE 2 THIOGUANINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 258-605; COMPND 5 SYNONYM: 41 KDA UBIQUITIN-SPECIFIC PROTEASE,DEUBIQUITINATING ENZYME COMPND 6 2,UBIQUITIN THIOESTERASE 2,UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 2; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 1-76; COMPND 13 SYNONYM: UBIQUITIN CARBOXYL EXTENSION PROTEIN 80 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP2, UBP41; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-24D; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 12 ORGANISM_COMMON: BOVINE; SOURCE 13 ORGANISM_TAXID: 9913 KEYWDS TERNARY COMPLEX, ESI COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.CHOU,S.J.CHUANG REVDAT 2 22-NOV-23 5XU8 1 LINK REVDAT 1 28-FEB-18 5XU8 0 JRNL AUTH S.J.CHUANG,S.C.CHENG,H.C.TANG,C.Y.SUN,C.Y.CHOU JRNL TITL 6-THIOGUANINE IS A NONCOMPETITIVE AND SLOW BINDING INHIBITOR JRNL TITL 2 OF HUMAN DEUBIQUITINATING PROTEASE USP2 JRNL REF SCI REP V. 8 3102 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29449607 JRNL DOI 10.1038/S41598-018-21476-W REMARK 2 REMARK 2 RESOLUTION. 1.81 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 33397 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) : 0.179 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1725 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4726 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 255 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3255 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.00000 REMARK 3 B22 (A**2) : -0.88000 REMARK 3 B33 (A**2) : 2.85000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.75000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.860 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3369 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4555 ; 1.487 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.233 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;31.190 ;23.274 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 607 ;14.842 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.815 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 499 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2565 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1621 ; 2.700 ; 3.633 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2024 ; 3.921 ; 5.434 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1747 ; 3.680 ; 4.062 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): 5283 ; 9.093 ;32.056 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5XU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300004185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL15A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.976 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33397 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 2HD5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24.5% PEG3350, 0.2 M MGC12, 0.1 M BIS REMARK 280 -TRIS, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 51.47650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.47650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.32500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 258 REMARK 465 ASN A 259 REMARK 465 SER A 260 REMARK 465 LYS A 261 REMARK 465 SER A 262 REMARK 465 ALA A 263 REMARK 465 THR A 377 REMARK 465 LEU A 378 REMARK 465 ARG A 379 REMARK 465 PRO A 380 REMARK 465 LYS A 381 REMARK 465 SER A 382 REMARK 465 ASN A 383 REMARK 465 PRO A 384 REMARK 465 GLU A 385 REMARK 465 SER A 600 REMARK 465 PRO A 601 REMARK 465 PRO A 602 REMARK 465 SER A 603 REMARK 465 ARG A 604 REMARK 465 MET A 605 REMARK 465 LEU A 606 REMARK 465 GLU A 607 REMARK 465 HIS A 608 REMARK 465 HIS A 609 REMARK 465 HIS A 610 REMARK 465 HIS A 611 REMARK 465 HIS A 612 REMARK 465 HIS A 613 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 908 O HOH A 908 2555 1.04 REMARK 500 REMARK 500 REMARK: NULL 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 363 NE - CZ - NH2 ANGL. DEV. = 3.1 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 HIS A 311 53.79 -37.72 REMARK 500 ARG A 448 -125.89 -66.35 REMARK 500 TYR A 450 -71.54 -71.07 REMARK 500 ILE A 510 -85.29 -106.42 REMARK 500 THR A 552 -169.51 -115.76 REMARK 500 ASP A 575 58.93 36.97 REMARK 500 SER A 576 -13.70 69.20 REMARK 500 THR B 7 -158.46 -92.38 REMARK 500 LEU B 71 -142.22 -111.13 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 NA A 709 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 309 OD1 REMARK 620 2 ASP A 413 OD1 58.6 REMARK 620 3 HOH A 940 O 131.2 154.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 706 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 403 OH REMARK 620 2 HOH A 991 O 92.0 REMARK 620 3 ALA B 46 O 98.2 111.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 707 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 421 OG REMARK 620 2 GLU B 64 O 115.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 425 SG REMARK 620 2 CYS A 428 SG 108.3 REMARK 620 3 CYS A 476 SG 105.7 104.6 REMARK 620 4 CYS A 479 SG 111.4 108.9 117.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 708 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 432 O REMARK 620 2 GLU B 64 OE1 104.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 705 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 506 O REMARK 620 2 SER A 508 O 113.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DX4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 103 DBREF 5XU8 A 258 605 UNP O75604 UBP2_HUMAN 258 605 DBREF 5XU8 B 1 76 UNP P62992 RS27A_BOVIN 1 76 SEQADV 5XU8 LEU A 606 UNP O75604 EXPRESSION TAG SEQADV 5XU8 GLU A 607 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 608 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 609 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 610 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 611 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 612 UNP O75604 EXPRESSION TAG SEQADV 5XU8 HIS A 613 UNP O75604 EXPRESSION TAG SEQRES 1 A 356 MET ASN SER LYS SER ALA GLN GLY LEU ALA GLY LEU ARG SEQRES 2 A 356 ASN LEU GLY ASN THR CYS PHE MET ASN SER ILE LEU GLN SEQRES 3 A 356 CYS LEU SER ASN THR ARG GLU LEU ARG ASP TYR CYS LEU SEQRES 4 A 356 GLN ARG LEU TYR MET ARG ASP LEU HIS HIS GLY SER ASN SEQRES 5 A 356 ALA HIS THR ALA LEU VAL GLU GLU PHE ALA LYS LEU ILE SEQRES 6 A 356 GLN THR ILE TRP THR SER SER PRO ASN ASP VAL VAL SER SEQRES 7 A 356 PRO SER GLU PHE LYS THR GLN ILE GLN ARG TYR ALA PRO SEQRES 8 A 356 ARG PHE VAL GLY TYR ASN GLN GLN ASP ALA GLN GLU PHE SEQRES 9 A 356 LEU ARG PHE LEU LEU ASP GLY LEU HIS ASN GLU VAL ASN SEQRES 10 A 356 ARG VAL THR LEU ARG PRO LYS SER ASN PRO GLU ASN LEU SEQRES 11 A 356 ASP HIS LEU PRO ASP ASP GLU LYS GLY ARG GLN MET TRP SEQRES 12 A 356 ARG LYS TYR LEU GLU ARG GLU ASP SER ARG ILE GLY ASP SEQRES 13 A 356 LEU PHE VAL GLY GLN LEU LYS SER SER LEU THR CYS THR SEQRES 14 A 356 ASP CYS GLY TYR CYS SER THR VAL PHE ASP PRO PHE TRP SEQRES 15 A 356 ASP LEU SER LEU PRO ILE ALA LYS ARG GLY TYR PRO GLU SEQRES 16 A 356 VAL THR LEU MET ASP CYS MET ARG LEU PHE THR LYS GLU SEQRES 17 A 356 ASP VAL LEU ASP GLY ASP GLU LYS PRO THR CYS CYS ARG SEQRES 18 A 356 CYS ARG GLY ARG LYS ARG CYS ILE LYS LYS PHE SER ILE SEQRES 19 A 356 GLN ARG PHE PRO LYS ILE LEU VAL LEU HIS LEU LYS ARG SEQRES 20 A 356 PHE SER GLU SER ARG ILE ARG THR SER LYS LEU THR THR SEQRES 21 A 356 PHE VAL ASN PHE PRO LEU ARG ASP LEU ASP LEU ARG GLU SEQRES 22 A 356 PHE ALA SER GLU ASN THR ASN HIS ALA VAL TYR ASN LEU SEQRES 23 A 356 TYR ALA VAL SER ASN HIS SER GLY THR THR MET GLY GLY SEQRES 24 A 356 HIS TYR THR ALA TYR CYS ARG SER PRO GLY THR GLY GLU SEQRES 25 A 356 TRP HIS THR PHE ASN ASP SER SER VAL THR PRO MET SER SEQRES 26 A 356 SER SER GLN VAL ARG THR SER ASP ALA TYR LEU LEU PHE SEQRES 27 A 356 TYR GLU LEU ALA SER PRO PRO SER ARG MET LEU GLU HIS SEQRES 28 A 356 HIS HIS HIS HIS HIS SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET DX4 A 701 11 HET ZN A 702 1 HET CL A 703 1 HET CL A 704 1 HET NA A 705 1 HET NA A 706 1 HET NA A 707 1 HET NA A 708 1 HET NA A 709 1 HET CL B 101 1 HET CL B 102 1 HET CL B 103 1 HETNAM DX4 2-AMINO-1,9-DIHYDRO-6H-PURINE-6-THIONE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION FORMUL 3 DX4 C5 H5 N5 S FORMUL 4 ZN ZN 2+ FORMUL 5 CL 5(CL 1-) FORMUL 7 NA 5(NA 1+) FORMUL 15 HOH *261(H2 O) HELIX 1 AA1 THR A 275 ASN A 287 1 13 HELIX 2 AA2 THR A 288 GLN A 297 1 10 HELIX 3 AA3 HIS A 311 TRP A 326 1 16 HELIX 4 AA4 PRO A 336 ALA A 347 1 12 HELIX 5 AA5 PRO A 348 VAL A 351 5 4 HELIX 6 AA6 ALA A 358 ASN A 374 1 17 HELIX 7 AA7 PRO A 391 GLU A 405 1 15 HELIX 8 AA8 SER A 409 VAL A 416 1 8 HELIX 9 AA9 LEU A 455 LYS A 464 1 10 HELIX 10 AB1 ASP A 469 LYS A 473 5 5 HELIX 11 AB2 ARG A 529 ALA A 532 5 4 HELIX 12 AB3 SER A 582 VAL A 586 5 5 HELIX 13 AB4 THR B 22 GLY B 35 1 14 HELIX 14 AB5 PRO B 37 GLN B 41 5 5 HELIX 15 AB6 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 2 GLY A 268 LEU A 269 0 SHEET 2 AA1 2 VAL A 333 VAL A 334 1 O VAL A 334 N GLY A 268 SHEET 1 AA2 2 GLN A 356 ASP A 357 0 SHEET 2 AA2 2 ARG B 74 GLY B 75 -1 O GLY B 75 N GLN A 356 SHEET 1 AA3 4 CYS A 431 PHE A 438 0 SHEET 2 AA3 4 GLY A 417 CYS A 425 -1 N LEU A 419 O ASP A 436 SHEET 3 AA3 4 CYS A 485 ARG A 493 -1 O ILE A 486 N THR A 424 SHEET 4 AA3 4 ASP A 466 LEU A 468 -1 N LEU A 468 O CYS A 485 SHEET 1 AA4 5 LEU A 441 LEU A 443 0 SHEET 2 AA4 5 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 AA4 5 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 AA4 5 VAL A 540 GLY A 551 -1 N ALA A 545 O PHE A 595 SHEET 5 AA4 5 LEU A 526 ASP A 527 -1 N LEU A 526 O TYR A 541 SHEET 1 AA5 7 LEU A 441 LEU A 443 0 SHEET 2 AA5 7 ILE A 497 LEU A 502 1 O HIS A 501 N LEU A 441 SHEET 3 AA5 7 ALA A 591 LEU A 598 -1 O LEU A 594 N LEU A 500 SHEET 4 AA5 7 VAL A 540 GLY A 551 -1 N ALA A 545 O PHE A 595 SHEET 5 AA5 7 GLY A 556 ARG A 563 -1 O HIS A 557 N SER A 550 SHEET 6 AA5 7 TRP A 570 ASN A 574 -1 O PHE A 573 N ALA A 560 SHEET 7 AA5 7 SER A 577 MET A 581 -1 O THR A 579 N THR A 572 SHEET 1 AA6 2 VAL A 453 THR A 454 0 SHEET 2 AA6 2 VAL A 519 ASN A 520 1 O ASN A 520 N VAL A 453 SHEET 1 AA7 2 THR A 475 CYS A 476 0 SHEET 2 AA7 2 GLY A 481 ARG A 482 -1 O GLY A 481 N CYS A 476 SHEET 1 AA8 5 THR B 12 GLU B 16 0 SHEET 2 AA8 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 AA8 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 AA8 5 ARG B 42 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA8 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK SG CYS A 276 S6 DX4 A 701 1555 1555 2.05 LINK OD1 ASN A 309 NA NA A 709 1555 1555 3.16 LINK OH TYR A 403 NA NA A 706 1555 1555 2.77 LINK OD1 ASP A 413 NA NA A 709 1555 4444 2.49 LINK OG SER A 421 NA NA A 707 1555 1555 2.74 LINK SG CYS A 425 ZN ZN A 702 1555 1555 2.33 LINK SG CYS A 428 ZN ZN A 702 1555 1555 2.34 LINK O SER A 432 NA NA A 708 1555 1555 2.84 LINK SG CYS A 476 ZN ZN A 702 1555 1555 2.40 LINK SG CYS A 479 ZN ZN A 702 1555 1555 2.36 LINK O SER A 506 NA NA A 705 1555 1555 3.02 LINK O SER A 508 NA NA A 705 1555 1555 2.67 LINK NA NA A 706 O HOH A 991 1555 1555 2.75 LINK NA NA A 706 O ALA B 46 1555 1555 2.63 LINK NA NA A 707 O GLU B 64 1555 1555 2.87 LINK NA NA A 708 OE1 GLU B 64 1555 1555 3.15 LINK NA NA A 709 O HOH A 940 1555 4454 2.54 SITE 1 AC1 11 LEU A 269 CYS A 276 ASN A 279 SER A 280 SITE 2 AC1 11 GLN A 283 TYR A 558 THR A 559 ALA A 560 SITE 3 AC1 11 PHE A 573 ASP A 575 SER A 576 SITE 1 AC2 4 CYS A 425 CYS A 428 CYS A 476 CYS A 479 SITE 1 AC3 4 SER A 513 LYS A 514 THR A 552 THR A 553 SITE 1 AC4 6 SER A 308 TRP A 400 ARG A 493 HOH A 891 SITE 2 AC4 6 HOH A 906 HOH A 947 SITE 1 AC5 4 SER A 506 GLU A 507 SER A 508 THR A 512 SITE 1 AC6 3 TYR A 403 HOH A 991 ALA B 46 SITE 1 AC7 4 SER A 421 LYS A 487 NA A 708 GLU B 64 SITE 1 AC8 5 SER A 421 LEU A 423 SER A 432 NA A 707 SITE 2 AC8 5 GLU B 64 SITE 1 AC9 6 SER A 308 ASN A 309 ASP A 408 SER A 409 SITE 2 AC9 6 ASP A 413 HOH A 940 SITE 1 AD1 6 HOH A 850 LYS B 27 GLN B 41 GLN B 49 SITE 2 AD1 6 HOH B 212 HOH B 222 SITE 1 AD2 6 GLU A 507 THR B 7 LEU B 8 THR B 9 SITE 2 AD2 6 GLY B 10 LYS B 11 SITE 1 AD3 2 THR B 22 ASN B 25 CRYST1 102.953 54.650 72.687 90.00 107.54 90.00 C 1 2 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 0.009713 0.000000 0.003070 0.00000 SCALE2 0.000000 0.018298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014429 0.00000