HEADER HYDROLASE 12-DEC-07 3BM4 TITLE CRYSTAL STRUCTURE OF HUMAN ADP-RIBOSE PYROPHOSPHATASE NUDT5 IN COMPLEX TITLE 2 WITH MAGNESIUM AND AMPCPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-SUGAR PYROPHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-210; COMPND 5 SYNONYM: NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 5, NUDIX MOTIF COMPND 6 5, YSA1H, ADP-RIBOSE PYROPHOSPHATASE NUDT5; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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, MOLECULAR KEYWDS 2 MECHANISM, SUBSTRATE SPECIFICITY, HYDROLASE, MAGNESIUM, KEYWDS 3 PHOSPHOPROTEIN, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR M.ZHA,Q.GUO,Y.ZHANG,C.ZHONG,Y.OU,J.DING REVDAT 5 01-NOV-23 3BM4 1 REMARK LINK REVDAT 4 25-OCT-17 3BM4 1 REMARK REVDAT 3 24-FEB-09 3BM4 1 VERSN REVDAT 2 03-JUN-08 3BM4 1 JRNL REVDAT 1 20-MAY-08 3BM4 0 JRNL AUTH M.ZHA,Q.GUO,Y.ZHANG,B.YU,Y.OU,C.ZHONG,J.DING JRNL TITL MOLECULAR MECHANISM OF ADP-RIBOSE HYDROLYSIS BY HUMAN NUDT5 JRNL TITL 2 FROM STRUCTURAL AND KINETIC STUDIES JRNL REF J.MOL.BIOL. V. 379 568 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18462755 JRNL DOI 10.1016/J.JMB.2008.04.006 REMARK 2 REMARK 2 RESOLUTION. 2.00 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1666449.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26400 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) : 0.198 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1319 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4156 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 221 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3030 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 331 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.12000 REMARK 3 B22 (A**2) : 9.73000 REMARK 3 B33 (A**2) : -6.61000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 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 : 0.34 REMARK 3 BSOL : 46.32 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.PARAMAM REMARK 3 PARAMETER FILE 4 : AMPCPR.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-07 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-17A 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 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26406 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.09300 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 2DSC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% PEG 4000, 0.25M 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 56.69700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.58400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.69700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.58400 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: 9150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 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 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 LYS A 210 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 LYS B 210 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 56 CG CD OE1 OE2 REMARK 470 GLN A 57 CG CD OE1 NE2 REMARK 470 GLU A 169 CG CD OE1 OE2 REMARK 470 GLU B 56 CG CD OE1 OE2 REMARK 470 GLN B 57 CG CD OE1 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 ASP A 133 76.01 -162.05 REMARK 500 ARG A 157 73.82 -119.01 REMARK 500 ASP A 177 34.16 -145.28 REMARK 500 ASN A 208 -86.25 -47.20 REMARK 500 ASP B 133 71.33 -162.96 REMARK 500 ASN B 208 73.00 61.05 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 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 96 O REMARK 620 2 GLU A 116 OE2 89.4 REMARK 620 3 HOH A 323 O 173.9 84.6 REMARK 620 4 HOH A 395 O 91.4 84.6 89.4 REMARK 620 5 ADV B 401 O1A 94.9 111.2 86.0 163.0 REMARK 620 6 ADV B 401 O2B 92.5 178.1 93.4 95.7 68.3 REMARK 620 N 1 2 3 4 5 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 HOH A 443 O 144.5 REMARK 620 3 ADV B 401 O1A 110.1 96.4 REMARK 620 N 1 2 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 OE1 REMARK 620 2 ADV B 401 O2A 95.8 REMARK 620 N 1 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 80.6 REMARK 620 3 ADV B 402 O2B 87.8 166.5 REMARK 620 4 ADV B 402 O1A 94.6 106.9 67.1 REMARK 620 5 HOH B 448 O 82.7 86.8 98.5 165.5 REMARK 620 6 HOH B 452 O 173.9 94.1 97.2 84.0 100.2 REMARK 620 N 1 2 3 4 5 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 116 OE1 REMARK 620 2 HOH B 449 O 99.6 REMARK 620 3 HOH B 562 O 69.3 89.5 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 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 ADV B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADV 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 REMARK 900 RELATED ID: 2DSD RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH MAGNESIUM AND AMP DBREF 3BM4 A 1 210 UNP Q9UKK9 NUDT5_HUMAN 1 210 DBREF 3BM4 B 1 210 UNP Q9UKK9 NUDT5_HUMAN 1 210 SEQRES 1 A 210 MET GLU SER GLN GLU PRO THR GLU SER SER GLN ASN GLY SEQRES 2 A 210 LYS GLN TYR ILE ILE SER GLU GLU LEU ILE SER GLU GLY SEQRES 3 A 210 LYS TRP VAL LYS LEU GLU LYS THR THR TYR MET ASP PRO SEQRES 4 A 210 THR GLY LYS THR ARG THR TRP GLU SER VAL LYS ARG THR SEQRES 5 A 210 THR ARG LYS GLU GLN THR ALA ASP GLY VAL ALA VAL ILE SEQRES 6 A 210 PRO VAL LEU GLN ARG THR LEU HIS TYR GLU CYS ILE VAL SEQRES 7 A 210 LEU VAL LYS GLN PHE ARG PRO PRO MET GLY GLY TYR CYS SEQRES 8 A 210 ILE GLU PHE PRO ALA GLY LEU ILE ASP ASP GLY GLU THR SEQRES 9 A 210 PRO GLU ALA ALA ALA LEU ARG GLU LEU GLU GLU GLU THR SEQRES 10 A 210 GLY TYR LYS GLY ASP ILE ALA GLU CYS SER PRO ALA VAL SEQRES 11 A 210 CYS MET ASP PRO GLY LEU SER ASN CYS THR ILE HIS ILE SEQRES 12 A 210 VAL THR VAL THR ILE ASN GLY ASP ASP ALA GLU ASN ALA SEQRES 13 A 210 ARG PRO LYS PRO LYS PRO GLY ASP GLY GLU PHE VAL GLU SEQRES 14 A 210 VAL ILE SER LEU PRO LYS ASN ASP LEU LEU GLN ARG LEU SEQRES 15 A 210 ASP ALA LEU VAL ALA GLU GLU HIS LEU THR VAL ASP ALA SEQRES 16 A 210 ARG VAL TYR SER TYR ALA LEU ALA LEU LYS HIS ALA ASN SEQRES 17 A 210 ALA LYS SEQRES 1 B 210 MET GLU SER GLN GLU PRO THR GLU SER SER GLN ASN GLY SEQRES 2 B 210 LYS GLN TYR ILE ILE SER GLU GLU LEU ILE SER GLU GLY SEQRES 3 B 210 LYS TRP VAL LYS LEU GLU LYS THR THR TYR MET ASP PRO SEQRES 4 B 210 THR GLY LYS THR ARG THR TRP GLU SER VAL LYS ARG THR SEQRES 5 B 210 THR ARG LYS GLU GLN THR ALA ASP GLY VAL ALA VAL ILE SEQRES 6 B 210 PRO VAL LEU GLN ARG THR LEU HIS TYR GLU CYS ILE VAL SEQRES 7 B 210 LEU VAL LYS GLN PHE ARG PRO PRO MET GLY GLY TYR CYS SEQRES 8 B 210 ILE GLU PHE PRO ALA GLY LEU ILE ASP ASP GLY GLU THR SEQRES 9 B 210 PRO GLU ALA ALA ALA LEU ARG GLU LEU GLU GLU GLU THR SEQRES 10 B 210 GLY TYR LYS GLY ASP ILE ALA GLU CYS SER PRO ALA VAL SEQRES 11 B 210 CYS MET ASP PRO GLY LEU SER ASN CYS THR ILE HIS ILE SEQRES 12 B 210 VAL THR VAL THR ILE ASN GLY ASP ASP ALA GLU ASN ALA SEQRES 13 B 210 ARG PRO LYS PRO LYS PRO GLY ASP GLY GLU PHE VAL GLU SEQRES 14 B 210 VAL ILE SER LEU PRO LYS ASN ASP LEU LEU GLN ARG LEU SEQRES 15 B 210 ASP ALA LEU VAL ALA GLU GLU HIS LEU THR VAL ASP ALA SEQRES 16 B 210 ARG VAL TYR SER TYR ALA LEU ALA LEU LYS HIS ALA ASN SEQRES 17 B 210 ALA LYS HET MG A 301 1 HET MG A 302 1 HET MG A 303 1 HET MG B 304 1 HET MG B 305 1 HET MG B 306 1 HET ADV B 401 36 HET ADV B 402 36 HETNAM MG MAGNESIUM ION HETNAM ADV ALPHA-BETA METHYLENE ADP-RIBOSE HETSYN ADV AMPCPR; {[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY- HETSYN 2 ADV TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY- HETSYN 3 ADV PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5- HETSYN 4 ADV TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER FORMUL 3 MG 6(MG 2+) FORMUL 9 ADV 2(C16 H25 N5 O13 P2) FORMUL 11 HOH *331(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 ALA A 209 1 16 HELIX 6 6 THR B 104 GLY B 118 1 15 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 GLU A 25 0 SHEET 2 A 3 VAL A 29 MET A 37 -1 O THR A 35 N ILE A 18 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 ARG A 70 -1 N VAL A 62 O GLY A 97 SHEET 3 B 5 HIS A 73 PHE A 83 -1 O CYS A 76 N LEU A 68 SHEET 4 B 5 TYR A 90 GLU A 93 -1 O CYS A 91 N GLN A 82 SHEET 5 B 5 LEU A 191 VAL A 193 1 O THR A 192 N ILE A 92 SHEET 1 C 5 ASP A 122 CYS A 126 0 SHEET 2 C 5 THR A 140 ASN A 149 -1 O THR A 145 N ALA A 124 SHEET 3 C 5 GLY A 61 ARG A 70 1 N VAL A 67 O VAL A 146 SHEET 4 C 5 HIS A 73 PHE A 83 -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 VAL A 130 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 CYS A 126 -1 N ALA A 124 O THR A 145 SHEET 1 E 3 TYR B 16 GLU B 25 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 TRP B 46 N THR B 34 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 CYS B 126 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 CYS B 126 -1 N ALA B 124 O THR B 145 LINK O ALA A 96 MG MG A 301 1555 1555 2.25 LINK OE2 GLU A 112 MG MG A 302 1555 1555 2.40 LINK OE1 GLU A 112 MG MG A 303 1555 1555 2.48 LINK OE2 GLU A 116 MG MG A 301 1555 1555 2.16 LINK MG MG A 301 O HOH A 323 1555 1555 2.41 LINK MG MG A 301 O HOH A 395 1555 1555 2.27 LINK MG MG A 301 O1A ADV B 401 1555 1555 2.37 LINK MG MG A 301 O2B ADV B 401 1555 1555 2.20 LINK MG MG A 302 O HOH A 443 1555 1555 2.45 LINK MG MG A 302 O1A ADV B 401 1555 1555 2.44 LINK MG MG A 303 O2A ADV B 401 1555 1555 2.34 LINK O ALA B 96 MG MG B 304 1555 1555 2.31 LINK OE1 GLU B 116 MG MG B 304 1555 1555 2.18 LINK OE1 GLU B 116 MG MG B 305 1555 1555 2.48 LINK MG MG B 304 O2B ADV B 402 1555 1555 2.12 LINK MG MG B 304 O1A ADV B 402 1555 1555 2.40 LINK MG MG B 304 O HOH B 448 1555 1555 2.25 LINK MG MG B 304 O HOH B 452 1555 1555 2.31 LINK MG MG B 305 O HOH B 449 1555 1555 2.49 LINK MG MG B 305 O HOH B 562 1555 1555 2.42 LINK MG MG B 306 O2A ADV B 402 1555 1555 2.46 SITE 1 AC1 4 ALA A 96 GLU A 116 HOH A 323 HOH A 395 SITE 1 AC2 5 GLU A 112 GLU A 116 HOH A 434 HOH A 438 SITE 2 AC2 5 HOH A 443 SITE 1 AC3 4 GLU A 112 HOH A 351 HOH A 362 HOH A 434 SITE 1 AC4 4 ALA B 96 GLU B 116 HOH B 448 HOH B 452 SITE 1 AC5 6 GLU B 112 GLU B 116 GLU B 166 HOH B 449 SITE 2 AC5 6 HOH B 512 HOH B 562 SITE 1 AC6 4 GLU B 112 HOH B 450 HOH B 491 HOH B 512 SITE 1 AC7 18 TRP A 28 ARG A 51 ARG A 84 ALA A 96 SITE 2 AC7 18 GLY A 97 LEU A 98 GLU A 112 MET A 132 SITE 3 AC7 18 GLU A 166 TRP B 46 GLU B 47 ASP B 133 SITE 4 AC7 18 GLY B 135 HOH B 437 HOH B 460 HOH B 463 SITE 5 AC7 18 HOH B 508 HOH B 551 SITE 1 AC8 20 TRP A 46 GLU A 47 ASP A 133 PRO A 134 SITE 2 AC8 20 GLY A 135 HOH A 348 TRP B 28 ARG B 51 SITE 3 AC8 20 ARG B 84 ALA B 96 GLY B 97 LEU B 98 SITE 4 AC8 20 GLU B 112 GLU B 116 MET B 132 GLU B 166 SITE 5 AC8 20 HOH B 425 HOH B 473 HOH B 488 HOH B 564 CRYST1 113.394 41.168 99.648 90.00 121.74 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 0.008819 0.000000 0.005456 0.00000 SCALE2 0.000000 0.024291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011800 0.00000