PDB Short entry for 2HD5 HEADER HYDROLASE 20-JUN-06 2HD5 TITLE USP2 IN COMPLEX WITH UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 258-605; COMPND 5 SYNONYM: UBIQUITIN THIOESTERASE 2, UBIQUITIN-SPECIFIC-PROCESSING COMPND 6 PROTEASE 2, DEUBIQUITINATING ENZYME 2, 41 KDA UBIQUITIN-SPECIFIC COMPND 7 PROTEASE; COMPND 8 EC: 3.1.2.15; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYUBIQUITIN; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: RESIDUES 1-76 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)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET24A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 13 ORGANISM_COMMON: CATTLE; SOURCE 14 ORGANISM_TAXID: 9913 KEYWDS DEUBIQUITINATING PROTEASE, CYSTEINE PROTEASE, SUBSTRATE ENZYME KEYWDS 2 COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.RENATUS,M.KROEMER REVDAT 5 30-AUG-23 2HD5 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2HD5 1 REMARK REVDAT 3 24-FEB-09 2HD5 1 VERSN REVDAT 2 22-AUG-06 2HD5 1 JRNL REVDAT 1 15-AUG-06 2HD5 0 JRNL AUTH M.RENATUS,S.G.PARRADO,A.D'ARCY,U.EIDHOFF,B.GERHARTZ, JRNL AUTH 2 U.HASSIEPEN,B.PIERRAT,R.RIEDL,D.VINZENZ,S.WORPENBERG, JRNL AUTH 3 M.KROEMER JRNL TITL STRUCTURAL BASIS OF UBIQUITIN RECOGNITION BY THE JRNL TITL 2 DEUBIQUITINATING PROTEASE USP2. JRNL REF STRUCTURE V. 14 1293 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16905103 JRNL DOI 10.1016/J.STR.2006.06.012 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2622971.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 28473 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1423 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1800 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1770 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1423 REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 28473 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3923 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 205 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.60000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -1.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.600 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.480 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.460 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.610 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 45.55 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MAX-FLUX MULTILAYER REMARK 200 OPTICS REMARK 200 OPTICS : CONFOCAL MAX-FLUX REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28474 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 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: 1OGW AND 1NBF, CHAIN C REMARK 200 REMARK 200 REMARK: CRYSTALS WERE DEHYDRATED PRIOR TO THE DATA COLLECTION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM MGCL2, 25% PEG 3550, 100 MM BIS REMARK 280 -TRIS, PROTEIN AT 11.8 MG/ML, PH 6.5, LIQUID DIFFUSION, REMARK 280 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 53.45150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.76700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 53.45150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.76700 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: 3830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 HOH A 160 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 MET A 205 REMARK 465 ASN A 206 REMARK 465 SER A 207 REMARK 465 LYS A 208 REMARK 465 SER A 209 REMARK 465 ALA A 210 REMARK 465 LEU A 246 REMARK 465 HIS A 247 REMARK 465 HIS A 248 REMARK 465 THR A 313B REMARK 465 LEU A 313C REMARK 465 ARG A 313D REMARK 465 PRO A 313E REMARK 465 LYS A 313F REMARK 465 SER A 313G REMARK 465 ASN A 313H REMARK 465 PRO A 313I REMARK 465 GLU A 313J REMARK 465 ASN A 313K REMARK 465 LEU A 313L REMARK 465 ASP A 313M REMARK 465 LYS A 355A REMARK 465 ARG A 355B REMARK 465 GLY A 355C REMARK 465 TYR A 355D REMARK 465 PRO A 355E REMARK 465 GLU A 355F REMARK 465 SER A 522 REMARK 465 PRO A 523 REMARK 465 PRO A 524 REMARK 465 SER A 525 REMARK 465 ARG A 526 REMARK 465 MET A 527 REMARK 465 ALA A 528 REMARK 465 ALA A 529 REMARK 465 ALA A 530 REMARK 465 LEU A 531 REMARK 465 GLU A 532 REMARK 465 HIS A 533 REMARK 465 HIS A 534 REMARK 465 HIS A 535 REMARK 465 HIS A 536 REMARK 465 HIS A 537 REMARK 465 HIS A 538 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 HIS A 313N CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 411 CG CD OE1 OE2 REMARK 470 SER A 412 OG REMARK 470 ARG A 413 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 416 CG1 CG2 CD1 REMARK 470 ARG A 417 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 365 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 PRO A 272 153.36 -48.44 REMARK 500 ASN A 272A 8.83 59.35 REMARK 500 ARG A 417 145.53 172.59 REMARK 500 ASN A 442 97.59 -22.74 REMARK 500 ALA A 446 87.26 -153.68 REMARK 500 ASP A 482 -121.77 41.06 REMARK 500 LEU B 71 -145.81 -108.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 284 0.07 SIDE CHAIN 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 334 SG REMARK 620 2 CYS A 337 SG 108.9 REMARK 620 3 CYS A 381 SG 108.6 104.8 REMARK 620 4 CYS A 384 SG 108.9 108.4 116.9 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 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NB8 RELATED DB: PDB REMARK 900 RELATED ID: 1NBF RELATED DB: PDB REMARK 900 RELATED ID: 2AYN RELATED DB: PDB REMARK 900 RELATED ID: 2AYO RELATED DB: PDB DBREF 2HD5 A 205 527 UNP O75604 UBP2_HUMAN 258 605 DBREF 2HD5 B 1 76 UNP Q24K23 Q24K23_BOVIN 1 76 SEQADV 2HD5 ALA A 528 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 ALA A 529 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 ALA A 530 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 LEU A 531 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 GLU A 532 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 533 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 534 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 535 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 536 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 537 UNP O75604 CLONING ARTIFACT SEQADV 2HD5 HIS A 538 UNP O75604 CLONING ARTIFACT SEQRES 1 A 359 MET ASN SER LYS SER ALA GLN GLY LEU ALA GLY LEU ARG SEQRES 2 A 359 ASN LEU GLY ASN THR CYS PHE MET ASN SER ILE LEU GLN SEQRES 3 A 359 CYS LEU SER ASN THR ARG GLU LEU ARG ASP TYR CYS LEU SEQRES 4 A 359 GLN ARG LEU TYR MET ARG ASP LEU HIS HIS GLY SER ASN SEQRES 5 A 359 ALA HIS THR ALA LEU VAL GLU GLU PHE ALA LYS LEU ILE SEQRES 6 A 359 GLN THR ILE TRP THR SER SER PRO ASN ASP VAL VAL SER SEQRES 7 A 359 PRO SER GLU PHE LYS THR GLN ILE GLN ARG TYR ALA PRO SEQRES 8 A 359 ARG PHE VAL GLY TYR ASN GLN GLN ASP ALA GLN GLU PHE SEQRES 9 A 359 LEU ARG PHE LEU LEU ASP GLY LEU HIS ASN GLU VAL ASN SEQRES 10 A 359 ARG VAL THR LEU ARG PRO LYS SER ASN PRO GLU ASN LEU SEQRES 11 A 359 ASP HIS LEU PRO ASP ASP GLU LYS GLY ARG GLN MET TRP SEQRES 12 A 359 ARG LYS TYR LEU GLU ARG GLU ASP SER ARG ILE GLY ASP SEQRES 13 A 359 LEU PHE VAL GLY GLN LEU LYS SER SER LEU THR CYS THR SEQRES 14 A 359 ASP CYS GLY TYR CYS SER THR VAL PHE ASP PRO PHE TRP SEQRES 15 A 359 ASP LEU SER LEU PRO ILE ALA LYS ARG GLY TYR PRO GLU SEQRES 16 A 359 VAL THR LEU MET ASP CYS MET ARG LEU PHE THR LYS GLU SEQRES 17 A 359 ASP VAL LEU ASP GLY ASP GLU LYS PRO THR CYS CYS ARG SEQRES 18 A 359 CYS ARG GLY ARG LYS ARG CYS ILE LYS LYS PHE SER ILE SEQRES 19 A 359 GLN ARG PHE PRO LYS ILE LEU VAL LEU HIS LEU LYS ARG SEQRES 20 A 359 PHE SER GLU SER ARG ILE ARG THR SER LYS LEU THR THR SEQRES 21 A 359 PHE VAL ASN PHE PRO LEU ARG ASP LEU ASP LEU ARG GLU SEQRES 22 A 359 PHE ALA SER GLU ASN THR ASN HIS ALA VAL TYR ASN LEU SEQRES 23 A 359 TYR ALA VAL SER ASN HIS SER GLY THR THR MET GLY GLY SEQRES 24 A 359 HIS TYR THR ALA TYR CYS ARG SER PRO GLY THR GLY GLU SEQRES 25 A 359 TRP HIS THR PHE ASN ASP SER SER VAL THR PRO MET SER SEQRES 26 A 359 SER SER GLN VAL ARG THR SER ASP ALA TYR LEU LEU PHE SEQRES 27 A 359 TYR GLU LEU ALA SER PRO PRO SER ARG MET ALA ALA ALA SEQRES 28 A 359 LEU GLU HIS 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 ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *160(H2 O) HELIX 1 1 THR A 222 ASN A 234 1 13 HELIX 2 2 THR A 235 GLN A 244 1 10 HELIX 3 3 ARG A 244A ASP A 245 1 6 HELIX 4 4 THR A 254 THR A 269 1 16 HELIX 5 5 PRO A 276 ALA A 285 1 12 HELIX 6 6 PRO A 286 VAL A 289 5 4 HELIX 7 7 ASP A 295 VAL A 311 1 17 HELIX 8 8 PRO A 313P GLU A 314D 1 15 HELIX 9 9 SER A 318 VAL A 325 1 8 HELIX 10 10 THR A 359 THR A 368 1 10 HELIX 11 11 ASP A 374 LYS A 378 5 5 HELIX 12 12 ARG A 434 ALA A 437 5 4 HELIX 13 13 SER A 489 VAL A 493 5 5 HELIX 14 14 THR B 22 GLY B 35 1 14 HELIX 15 15 THR B 55 ASN B 60 5 6 SHEET 1 A 2 GLY A 215 LEU A 216 0 SHEET 2 A 2 VAL A 273 VAL A 274 1 O VAL A 274 N GLY A 215 SHEET 1 B 4 CYS A 340 PHE A 347 0 SHEET 2 B 4 GLY A 326 CYS A 334 -1 N LEU A 332 O SER A 341 SHEET 3 B 4 CYS A 389 ARG A 397 -1 O SER A 394 N LYS A 329 SHEET 4 B 4 ASP A 371 LEU A 373 -1 N LEU A 373 O CYS A 389 SHEET 1 C 5 LEU A 350 PRO A 353 0 SHEET 2 C 5 ILE A 401 LYS A 407 1 O HIS A 405 N LEU A 350 SHEET 3 C 5 ALA A 513 LEU A 520 -1 O LEU A 516 N LEU A 404 SHEET 4 C 5 VAL A 447 GLY A 458 -1 N ALA A 452 O PHE A 517 SHEET 5 C 5 LEU A 431 ASP A 432 -1 N LEU A 431 O TYR A 448 SHEET 1 D 7 LEU A 350 PRO A 353 0 SHEET 2 D 7 ILE A 401 LYS A 407 1 O HIS A 405 N LEU A 350 SHEET 3 D 7 ALA A 513 LEU A 520 -1 O LEU A 516 N LEU A 404 SHEET 4 D 7 VAL A 447 GLY A 458 -1 N ALA A 452 O PHE A 517 SHEET 5 D 7 GLY A 463 ARG A 470 -1 O ARG A 470 N TYR A 451 SHEET 6 D 7 TRP A 477 ASN A 481 -1 O PHE A 480 N ALA A 467 SHEET 7 D 7 SER A 484 MET A 488 -1 O THR A 486 N THR A 479 SHEET 1 E 2 THR A 380 CYS A 381 0 SHEET 2 E 2 GLY A 385 ARG A 386 -1 O GLY A 385 N CYS A 381 SHEET 1 F 5 THR B 12 GLU B 16 0 SHEET 2 F 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 F 5 THR B 66 VAL B 70 1 O LEU B 67 N PHE B 4 SHEET 4 F 5 ARG B 42 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 F 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 LINK ZN ZN A 201 SG CYS A 334 1555 1555 2.46 LINK ZN ZN A 201 SG CYS A 337 1555 1555 2.32 LINK ZN ZN A 201 SG CYS A 381 1555 1555 2.36 LINK ZN ZN A 201 SG CYS A 384 1555 1555 2.40 SITE 1 AC1 4 CYS A 334 CYS A 337 CYS A 381 CYS A 384 CRYST1 106.903 45.534 76.360 90.00 110.01 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 0.009354 0.000000 0.003407 0.00000 SCALE2 0.000000 0.021962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013937 0.00000