HEADER HYDROLASE 28-JUN-06 2DSD TITLE CRYSTAL STRUCTURE OF HUMAN ADP-RIBOSE PYROPHOSPHATASE NUDT5 IN COMPLEX TITLE 2 WITH MAGNESIUM AND AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-SUGAR PYROPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-210; COMPND 5 SYNONYM: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 5, NUDIX MOTIF COMPND 6 5, YSA1H; COMPND 7 EC: 3.6.1.13, 3.6.1.-; 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: NUDT5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1 KEYWDS NUDIX DOMAIN, ADPR, ADP-RIBOSE PYROPHOSPHATASE, NUDT5, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHA,C.ZHONG,J.DING REVDAT 4 25-OCT-23 2DSD 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2DSD 1 VERSN REVDAT 2 12-DEC-06 2DSD 1 JRNL REVDAT 1 14-NOV-06 2DSD 0 JRNL AUTH M.ZHA,C.ZHONG,Y.PENG,H.HU,J.DING JRNL TITL CRYSTAL STRUCTURES OF HUMAN NUDT5 REVEAL INSIGHTS INTO THE JRNL TITL 2 STRUCTURAL BASIS OF THE SUBSTRATE SPECIFICITY JRNL REF J.MOL.BIOL. V. 364 1021 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 17052728 JRNL DOI 10.1016/J.JMB.2006.09.078 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1134788.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 11735 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 SET) : 0.215 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 600 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1703 REMARK 3 BIN R VALUE (WORKING SET) : 0.3610 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 94 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3032 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.78000 REMARK 3 B22 (A**2) : 12.40000 REMARK 3 B33 (A**2) : -4.61000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.65000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.45 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.49 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 41.90 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 : AMP2.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : AMP2.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DSD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000025786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12038 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 2DSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.2M SODIUM ACETATE, REMARK 280 0.1M TRIS HYDROCHLORIDE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 56.03800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.07800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.03800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.07800 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: 8400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 GLN A 4 REMARK 465 GLU A 5 REMARK 465 PRO A 6 REMARK 465 THR A 7 REMARK 465 GLU A 8 REMARK 465 SER A 9 REMARK 465 SER A 10 REMARK 465 GLN A 11 REMARK 465 ASN A 12 REMARK 465 GLY A 13 REMARK 465 ALA A 209 REMARK 465 LYS A 210 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 GLN B 4 REMARK 465 GLU B 5 REMARK 465 PRO B 6 REMARK 465 THR B 7 REMARK 465 GLU B 8 REMARK 465 SER B 9 REMARK 465 SER B 10 REMARK 465 GLN B 11 REMARK 465 ASN B 12 REMARK 465 GLY B 13 REMARK 465 ALA B 209 REMARK 465 LYS B 210 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 LYS A 55 -83.11 -125.74 REMARK 500 ASP A 133 74.39 -161.38 REMARK 500 LEU A 136 -44.97 -135.85 REMARK 500 SER B 19 141.56 -170.13 REMARK 500 TRP B 46 126.29 -178.25 REMARK 500 LYS B 55 -133.34 -112.24 REMARK 500 GLN B 57 -154.98 -109.13 REMARK 500 ASP B 133 88.81 -162.39 REMARK 500 LEU B 136 -36.76 -153.28 REMARK 500 ASP B 177 22.45 -140.92 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 112 OE2 REMARK 620 2 GLU A 116 OE2 107.8 REMARK 620 3 GLU A 166 OE1 163.2 88.7 REMARK 620 4 GLU A 166 OE2 147.6 65.3 42.8 REMARK 620 5 AMP A 401 O1P 65.3 70.5 125.4 83.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 112 OE2 REMARK 620 2 AMP A 401 O1P 65.3 REMARK 620 3 HOH A 431 O 50.9 90.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 116 OE1 REMARK 620 2 GLU A 116 OE2 46.3 REMARK 620 3 AMP A 401 O2P 99.9 53.6 REMARK 620 4 HOH A 417 O 133.4 95.0 48.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 96 O REMARK 620 2 GLU B 116 OE1 62.6 REMARK 620 3 AMP B 402 O3P 71.1 65.1 REMARK 620 4 HOH B 419 O 74.7 137.2 101.1 REMARK 620 5 HOH B 440 O 158.4 115.3 88.3 103.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 112 OE1 REMARK 620 2 GLU B 116 OE1 88.1 REMARK 620 3 GLU B 166 OE1 160.1 74.6 REMARK 620 4 GLU B 166 OE2 154.7 111.4 45.0 REMARK 620 5 AMP B 402 O3P 89.5 63.1 74.2 113.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 112 OE2 REMARK 620 2 AMP B 402 O2P 74.9 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 MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DSB RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT LIGANDS REMARK 900 RELATED ID: 2DSC RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND ADP-RIBOSE DBREF 2DSD A 1 210 UNP Q9UKK9 NUDT5_HUMAN 1 210 DBREF 2DSD B 1 210 UNP Q9UKK9 NUDT5_HUMAN 1 210 SEQADV 2DSD GLY A -1 UNP Q9UKK9 CLONING ARTIFACT SEQADV 2DSD SER A 0 UNP Q9UKK9 CLONING ARTIFACT SEQADV 2DSD GLY B -1 UNP Q9UKK9 CLONING ARTIFACT SEQADV 2DSD SER B 0 UNP Q9UKK9 CLONING ARTIFACT SEQRES 1 A 212 GLY SER MET GLU SER GLN GLU PRO THR GLU SER SER GLN SEQRES 2 A 212 ASN GLY LYS GLN TYR ILE ILE SER GLU GLU LEU ILE SER SEQRES 3 A 212 GLU GLY LYS TRP VAL LYS LEU GLU LYS THR THR TYR MET SEQRES 4 A 212 ASP PRO THR GLY LYS THR ARG THR TRP GLU SER VAL LYS SEQRES 5 A 212 ARG THR THR ARG LYS GLU GLN THR ALA ASP GLY VAL ALA SEQRES 6 A 212 VAL ILE PRO VAL LEU GLN ARG THR LEU HIS TYR GLU CYS SEQRES 7 A 212 ILE VAL LEU VAL LYS GLN PHE ARG PRO PRO MET GLY GLY SEQRES 8 A 212 TYR CYS ILE GLU PHE PRO ALA GLY LEU ILE ASP ASP GLY SEQRES 9 A 212 GLU THR PRO GLU ALA ALA ALA LEU ARG GLU LEU GLU GLU SEQRES 10 A 212 GLU THR GLY TYR LYS GLY ASP ILE ALA GLU CYS SER PRO SEQRES 11 A 212 ALA VAL CYS MET ASP PRO GLY LEU SER ASN CYS THR ILE SEQRES 12 A 212 HIS ILE VAL THR VAL THR ILE ASN GLY ASP ASP ALA GLU SEQRES 13 A 212 ASN ALA ARG PRO LYS PRO LYS PRO GLY ASP GLY GLU PHE SEQRES 14 A 212 VAL GLU VAL ILE SER LEU PRO LYS ASN ASP LEU LEU GLN SEQRES 15 A 212 ARG LEU ASP ALA LEU VAL ALA GLU GLU HIS LEU THR VAL SEQRES 16 A 212 ASP ALA ARG VAL TYR SER TYR ALA LEU ALA LEU LYS HIS SEQRES 17 A 212 ALA ASN ALA LYS SEQRES 1 B 212 GLY SER MET GLU SER GLN GLU PRO THR GLU SER SER GLN SEQRES 2 B 212 ASN GLY LYS GLN TYR ILE ILE SER GLU GLU LEU ILE SER SEQRES 3 B 212 GLU GLY LYS TRP VAL LYS LEU GLU LYS THR THR TYR MET SEQRES 4 B 212 ASP PRO THR GLY LYS THR ARG THR TRP GLU SER VAL LYS SEQRES 5 B 212 ARG THR THR ARG LYS GLU GLN THR ALA ASP GLY VAL ALA SEQRES 6 B 212 VAL ILE PRO VAL LEU GLN ARG THR LEU HIS TYR GLU CYS SEQRES 7 B 212 ILE VAL LEU VAL LYS GLN PHE ARG PRO PRO MET GLY GLY SEQRES 8 B 212 TYR CYS ILE GLU PHE PRO ALA GLY LEU ILE ASP ASP GLY SEQRES 9 B 212 GLU THR PRO GLU ALA ALA ALA LEU ARG GLU LEU GLU GLU SEQRES 10 B 212 GLU THR GLY TYR LYS GLY ASP ILE ALA GLU CYS SER PRO SEQRES 11 B 212 ALA VAL CYS MET ASP PRO GLY LEU SER ASN CYS THR ILE SEQRES 12 B 212 HIS ILE VAL THR VAL THR ILE ASN GLY ASP ASP ALA GLU SEQRES 13 B 212 ASN ALA ARG PRO LYS PRO LYS PRO GLY ASP GLY GLU PHE SEQRES 14 B 212 VAL GLU VAL ILE SER LEU PRO LYS ASN ASP LEU LEU GLN SEQRES 15 B 212 ARG LEU ASP ALA LEU VAL ALA GLU GLU HIS LEU THR VAL SEQRES 16 B 212 ASP ALA ARG VAL TYR SER TYR ALA LEU ALA LEU LYS HIS SEQRES 17 B 212 ALA ASN ALA LYS HET MG A 301 1 HET MG A 302 1 HET MG A 303 1 HET AMP A 401 23 HET MG B 304 1 HET MG B 305 1 HET MG B 306 1 HET AMP B 402 23 HETNAM MG MAGNESIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 3 MG 6(MG 2+) FORMUL 6 AMP 2(C10 H14 N5 O7 P) FORMUL 11 HOH *96(H2 O) HELIX 1 1 PRO A 85 GLY A 88 5 4 HELIX 2 2 THR A 104 GLY A 118 1 15 HELIX 3 3 ASP A 152 ALA A 156 5 5 HELIX 4 4 ASP A 177 GLU A 189 1 13 HELIX 5 5 ASP A 194 ASN A 208 1 15 HELIX 6 6 THR B 104 THR B 117 1 14 HELIX 7 7 ASP B 152 ALA B 156 5 5 HELIX 8 8 ASP B 177 GLU B 189 1 13 HELIX 9 9 ASP B 194 ALA B 207 1 14 SHEET 1 A 3 TYR A 16 SER A 24 0 SHEET 2 A 3 VAL A 29 MET A 37 -1 O LYS A 33 N GLU A 21 SHEET 3 A 3 THR A 43 ARG A 51 -1 O TRP A 46 N THR A 34 SHEET 1 B 5 ALA A 96 LEU A 98 0 SHEET 2 B 5 GLY A 61 GLN A 69 -1 N VAL A 62 O GLY A 97 SHEET 3 B 5 CYS A 76 ARG A 84 -1 O CYS A 76 N LEU A 68 SHEET 4 B 5 GLY A 89 GLU A 93 -1 O GLY A 89 N ARG A 84 SHEET 5 B 5 THR A 192 VAL A 193 1 O THR A 192 N ILE A 92 SHEET 1 C 5 ASP A 122 GLU A 125 0 SHEET 2 C 5 THR A 140 ASN A 149 -1 O THR A 147 N ASP A 122 SHEET 3 C 5 GLY A 61 GLN A 69 1 N GLN A 69 O ILE A 148 SHEET 4 C 5 CYS A 76 ARG A 84 -1 O CYS A 76 N LEU A 68 SHEET 5 C 5 GLU A 169 PRO A 174 -1 O LEU A 173 N ILE A 77 SHEET 1 D 3 ALA A 129 CYS A 131 0 SHEET 2 D 3 THR A 140 ASN A 149 -1 O ILE A 141 N VAL A 130 SHEET 3 D 3 ASP A 122 GLU A 125 -1 N ASP A 122 O THR A 147 SHEET 1 E 3 TYR B 16 SER B 24 0 SHEET 2 E 3 VAL B 29 MET B 37 -1 O LYS B 33 N GLU B 21 SHEET 3 E 3 THR B 43 ARG B 51 -1 O ARG B 44 N TYR B 36 SHEET 1 F 5 ALA B 96 LEU B 98 0 SHEET 2 F 5 GLY B 61 GLN B 69 -1 N VAL B 62 O GLY B 97 SHEET 3 F 5 CYS B 76 PHE B 83 -1 O CYS B 76 N LEU B 68 SHEET 4 F 5 TYR B 90 GLU B 93 -1 O GLU B 93 N VAL B 80 SHEET 5 F 5 THR B 192 VAL B 193 1 O THR B 192 N ILE B 92 SHEET 1 G 5 ASP B 122 GLU B 125 0 SHEET 2 G 5 THR B 140 ASN B 149 -1 O THR B 145 N ALA B 124 SHEET 3 G 5 GLY B 61 GLN B 69 1 N GLN B 69 O ILE B 148 SHEET 4 G 5 CYS B 76 PHE B 83 -1 O CYS B 76 N LEU B 68 SHEET 5 G 5 GLU B 169 PRO B 174 -1 O LEU B 173 N ILE B 77 SHEET 1 H 3 VAL B 130 CYS B 131 0 SHEET 2 H 3 THR B 140 ASN B 149 -1 O ILE B 141 N VAL B 130 SHEET 3 H 3 ASP B 122 GLU B 125 -1 N ALA B 124 O THR B 145 LINK OE2 GLU A 112 MG MG A 302 1555 1555 2.95 LINK OE2 GLU A 112 MG MG A 303 1555 1555 2.90 LINK OE1 GLU A 116 MG MG A 301 1555 1555 2.74 LINK OE2 GLU A 116 MG MG A 301 1555 1555 2.86 LINK OE2 GLU A 116 MG MG A 302 1555 1555 2.97 LINK OE1 GLU A 166 MG MG A 302 1555 1555 3.04 LINK OE2 GLU A 166 MG MG A 302 1555 1555 2.97 LINK MG MG A 301 O2P AMP A 401 1555 1555 2.76 LINK MG MG A 301 O HOH A 417 1555 1555 2.95 LINK MG MG A 302 O1P AMP A 401 1555 1555 2.65 LINK MG MG A 303 O1P AMP A 401 1555 1555 2.71 LINK MG MG A 303 O HOH A 431 1555 1555 3.08 LINK O ALA B 96 MG MG B 304 1555 1555 2.50 LINK OE1 GLU B 112 MG MG B 305 1555 1555 2.41 LINK OE2 GLU B 112 MG MG B 306 1555 1555 2.71 LINK OE1 GLU B 116 MG MG B 304 1555 1555 2.50 LINK OE1 GLU B 116 MG MG B 305 1555 1555 2.65 LINK OE1 GLU B 166 MG MG B 305 1555 1555 2.72 LINK OE2 GLU B 166 MG MG B 305 1555 1555 3.00 LINK MG MG B 304 O3P AMP B 402 1555 1555 2.69 LINK MG MG B 304 O HOH B 419 1555 1555 2.95 LINK MG MG B 304 O HOH B 440 1555 1555 2.90 LINK MG MG B 305 O3P AMP B 402 1555 1555 2.70 LINK MG MG B 306 O2P AMP B 402 1555 1555 2.75 SITE 1 AC1 6 GLN A 82 ARG A 84 ALA A 96 GLU A 116 SITE 2 AC1 6 AMP A 401 HOH A 417 SITE 1 AC2 5 GLU A 112 GLU A 115 GLU A 116 GLU A 166 SITE 2 AC2 5 AMP A 401 SITE 1 AC3 4 LEU A 98 GLU A 112 AMP A 401 HOH A 431 SITE 1 AC4 6 ALA B 96 GLU B 116 GLU B 166 AMP B 402 SITE 2 AC4 6 HOH B 419 HOH B 440 SITE 1 AC5 4 GLU B 112 GLU B 116 GLU B 166 AMP B 402 SITE 1 AC6 2 GLU B 112 AMP B 402 SITE 1 AC7 12 TRP A 28 ALA A 96 GLY A 97 GLU A 112 SITE 2 AC7 12 GLU A 116 GLU A 166 MG A 301 MG A 302 SITE 3 AC7 12 MG A 303 HOH A 417 TRP B 46 GLU B 47 SITE 1 AC8 16 THR A 45 TRP A 46 GLU A 47 VAL B 29 SITE 2 AC8 16 ARG B 51 ALA B 96 GLY B 97 LEU B 98 SITE 3 AC8 16 GLU B 112 GLU B 116 GLU B 166 MG B 304 SITE 4 AC8 16 MG B 305 MG B 306 HOH B 419 HOH B 442 CRYST1 112.076 40.156 100.124 90.00 121.68 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 0.008923 0.000000 0.005505 0.00000 SCALE2 0.000000 0.024903 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011736 0.00000