PDB Short entry for 3KJD HEADER TRANSFERASE 03-NOV-09 3KJD TITLE HUMAN POLY(ADP-RIBOSE) POLYMERASE 2, CATALYTIC FRAGMENT IN COMPLEX TITLE 2 WITH AN INHIBITOR ABT-888 COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY [ADP-RIBOSE] POLYMERASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: PARP-2, NAD(+) ADP-RIBOSYLTRANSFERASE 2, POLY[ADP-RIBOSE] COMPND 6 SYNTHETASE 2, PADPRT-2, HPARP-2; COMPND 7 EC: 2.4.2.30; 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: ADPRT2, ADPRTL2, PARP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)R2 PRARE; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE, ENZYME-INHIBITOR COMPLEX, CATALYTIC FRAGMENT, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, GLYCOSYLTRANSFERASE, KEYWDS 3 NAD, NUCLEUS, DNA-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR T.KARLBERG,P.SCHUTZ,C.H.ARROWSMITH,H.BERGLUND,C.BOUNTRA,R.COLLINS, AUTHOR 2 A.M.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,A.JOHANSSON, AUTHOR 3 I.JOHANSSON,A.KALLAS,T.KOTENYOVA,A.KOTZSCH,P.KRAULIS,T.K.NIELSEN, AUTHOR 4 M.MOCHE,P.NORDLUND,T.NYMAN,C.PERSSON,A.K.ROOS,M.I.SIPONEN, AUTHOR 5 A.G.THORSELL,L.TRESAUGUES,S.VAN DEN BERG,J.WEIGELT,M.WELIN, AUTHOR 6 M.WISNIEWSKA,H.SCHULER,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 13-JUL-11 3KJD 1 VERSN REVDAT 2 31-MAR-10 3KJD 1 JRNL REVDAT 1 17-NOV-09 3KJD 0 JRNL AUTH T.KARLBERG,M.HAMMARSTROM,P.SCHUTZ,L.SVENSSON,H.SCHULER JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN PARP2 IN JRNL TITL 2 COMPLEX WITH PARP INHIBITOR ABT-888. JRNL REF BIOCHEMISTRY V. 49 1056 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20092359 JRNL DOI 10.1021/BI902079Y REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 54581 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 : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2873 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4029 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 212 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : 0.18000 REMARK 3 B33 (A**2) : -0.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.160 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.639 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5735 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3936 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7743 ; 1.488 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9602 ; 0.919 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 700 ; 6.102 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 258 ;36.663 ;24.419 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1035 ;13.772 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;18.662 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 846 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6287 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1106 ; 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): 3494 ; 0.912 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1418 ; 0.236 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5611 ; 1.665 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2241 ; 2.661 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2131 ; 4.334 ; 4.500 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 : 1.40 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 REMARK 4 REMARK 4 3KJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-09. REMARK 100 THE RCSB ID CODE IS RCSB056064. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57455 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 41.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.09600 REMARK 200 R SYM (I) : 0.12500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : 0.58200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3KCZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M TRIS, 0.25M NACL, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 67.30550 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 HIS A 217 REMARK 465 HIS A 218 REMARK 465 SER A 219 REMARK 465 SER A 220 REMARK 465 GLY A 221 REMARK 465 VAL A 222 REMARK 465 ASP A 223 REMARK 465 LEU A 224 REMARK 465 GLY A 225 REMARK 465 THR A 349 REMARK 465 GLU A 350 REMARK 465 LEU A 351 REMARK 465 GLN A 352 REMARK 465 MET B 212 REMARK 465 HIS B 213 REMARK 465 HIS B 214 REMARK 465 HIS B 215 REMARK 465 HIS B 216 REMARK 465 HIS B 217 REMARK 465 HIS B 218 REMARK 465 SER B 219 REMARK 465 SER B 220 REMARK 465 GLY B 221 REMARK 465 VAL B 222 REMARK 465 LEU B 547 REMARK 465 ASN B 548 REMARK 465 PRO B 549 REMARK 465 ASP B 550 REMARK 465 GLY B 551 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 ASN A 228 CG OD1 REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 GLN A 510 CD OE1 NE2 REMARK 470 LEU A 547 CG CD1 CD2 REMARK 470 TYR A 552 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 296 CD NE CZ NH1 NH2 REMARK 470 TYR B 552 CG CD1 CD2 CE1 CE2 CZ OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 615 O HOH A 650 2.03 REMARK 500 OG1 THR A 323 O HOH A 709 2.16 REMARK 500 O HOH B 77 O HOH B 630 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 NE2 GLN B 232 OD1 ASN B 502 1655 2.14 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 316 NE - CZ - NH2 ANGL. DEV. = -3.3 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 294 -13.21 -140.95 REMARK 500 HIS A 394 51.28 -110.10 REMARK 500 PRO A 549 59.96 -95.56 REMARK 500 ASP A 550 -46.85 -158.17 REMARK 500 ARG A 570 -37.71 -130.12 REMARK 500 MET B 234 142.45 -32.08 REMARK 500 ARG B 322 -19.30 -140.58 REMARK 500 HIS B 394 55.23 -109.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 671 DISTANCE = 5.09 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 78P A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 580 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 78P B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KCZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 3-AMINOBENZAMIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FEATURE OF UNIPROT (Q9UGN5, PARP2_HUMAN) SHOWS P -> H (IN REF. REMARK 999 2; AAD29857) AT THIS POSITION. DBREF 3KJD A 235 579 UNP Q9UGN5 PARP2_HUMAN 235 579 DBREF 3KJD B 235 579 UNP Q9UGN5 PARP2_HUMAN 235 579 SEQADV 3KJD MET A 212 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 213 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 214 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 215 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 216 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 217 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 218 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER A 219 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER A 220 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLY A 221 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD VAL A 222 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD ASP A 223 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD LEU A 224 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLY A 225 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD THR A 226 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLU A 227 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD ASN A 228 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD LEU A 229 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD TYR A 230 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD PHE A 231 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLN A 232 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER A 233 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD MET A 234 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS A 447 UNP Q9UGN5 PRO 447 SEE REMARK 999 SEQADV 3KJD MET B 212 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 213 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 214 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 215 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 216 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 217 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 218 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER B 219 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER B 220 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLY B 221 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD VAL B 222 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD ASP B 223 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD LEU B 224 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLY B 225 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD THR B 226 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLU B 227 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD ASN B 228 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD LEU B 229 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD TYR B 230 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD PHE B 231 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD GLN B 232 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD SER B 233 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD MET B 234 UNP Q9UGN5 EXPRESSION TAG SEQADV 3KJD HIS B 447 UNP Q9UGN5 PRO 447 SEE REMARK 999 SEQRES 1 A 368 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 368 GLY THR GLU ASN LEU TYR PHE GLN SER MET ASP LEU ARG SEQRES 3 A 368 VAL GLN GLU LEU ILE LYS LEU ILE CYS ASN VAL GLN ALA SEQRES 4 A 368 MET GLU GLU MET MET MET GLU MET LYS TYR ASN THR LYS SEQRES 5 A 368 LYS ALA PRO LEU GLY LYS LEU THR VAL ALA GLN ILE LYS SEQRES 6 A 368 ALA GLY TYR GLN SER LEU LYS LYS ILE GLU ASP CYS ILE SEQRES 7 A 368 ARG ALA GLY GLN HIS GLY ARG ALA LEU MET GLU ALA CYS SEQRES 8 A 368 ASN GLU PHE TYR THR ARG ILE PRO HIS ASP PHE GLY LEU SEQRES 9 A 368 ARG THR PRO PRO LEU ILE ARG THR GLN LYS GLU LEU SER SEQRES 10 A 368 GLU LYS ILE GLN LEU LEU GLU ALA LEU GLY ASP ILE GLU SEQRES 11 A 368 ILE ALA ILE LYS LEU VAL LYS THR GLU LEU GLN SER PRO SEQRES 12 A 368 GLU HIS PRO LEU ASP GLN HIS TYR ARG ASN LEU HIS CYS SEQRES 13 A 368 ALA LEU ARG PRO LEU ASP HIS GLU SER TYR GLU PHE LYS SEQRES 14 A 368 VAL ILE SER GLN TYR LEU GLN SER THR HIS ALA PRO THR SEQRES 15 A 368 HIS SER ASP TYR THR MET THR LEU LEU ASP LEU PHE GLU SEQRES 16 A 368 VAL GLU LYS ASP GLY GLU LYS GLU ALA PHE ARG GLU ASP SEQRES 17 A 368 LEU HIS ASN ARG MET LEU LEU TRP HIS GLY SER ARG MET SEQRES 18 A 368 SER ASN TRP VAL GLY ILE LEU SER HIS GLY LEU ARG ILE SEQRES 19 A 368 ALA HIS PRO GLU ALA PRO ILE THR GLY TYR MET PHE GLY SEQRES 20 A 368 LYS GLY ILE TYR PHE ALA ASP MET SER SER LYS SER ALA SEQRES 21 A 368 ASN TYR CYS PHE ALA SER ARG LEU LYS ASN THR GLY LEU SEQRES 22 A 368 LEU LEU LEU SER GLU VAL ALA LEU GLY GLN CYS ASN GLU SEQRES 23 A 368 LEU LEU GLU ALA ASN PRO LYS ALA GLU GLY LEU LEU GLN SEQRES 24 A 368 GLY LYS HIS SER THR LYS GLY LEU GLY LYS MET ALA PRO SEQRES 25 A 368 SER SER ALA HIS PHE VAL THR LEU ASN GLY SER THR VAL SEQRES 26 A 368 PRO LEU GLY PRO ALA SER ASP THR GLY ILE LEU ASN PRO SEQRES 27 A 368 ASP GLY TYR THR LEU ASN TYR ASN GLU TYR ILE VAL TYR SEQRES 28 A 368 ASN PRO ASN GLN VAL ARG MET ARG TYR LEU LEU LYS VAL SEQRES 29 A 368 GLN PHE ASN PHE SEQRES 1 B 368 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 368 GLY THR GLU ASN LEU TYR PHE GLN SER MET ASP LEU ARG SEQRES 3 B 368 VAL GLN GLU LEU ILE LYS LEU ILE CYS ASN VAL GLN ALA SEQRES 4 B 368 MET GLU GLU MET MET MET GLU MET LYS TYR ASN THR LYS SEQRES 5 B 368 LYS ALA PRO LEU GLY LYS LEU THR VAL ALA GLN ILE LYS SEQRES 6 B 368 ALA GLY TYR GLN SER LEU LYS LYS ILE GLU ASP CYS ILE SEQRES 7 B 368 ARG ALA GLY GLN HIS GLY ARG ALA LEU MET GLU ALA CYS SEQRES 8 B 368 ASN GLU PHE TYR THR ARG ILE PRO HIS ASP PHE GLY LEU SEQRES 9 B 368 ARG THR PRO PRO LEU ILE ARG THR GLN LYS GLU LEU SER SEQRES 10 B 368 GLU LYS ILE GLN LEU LEU GLU ALA LEU GLY ASP ILE GLU SEQRES 11 B 368 ILE ALA ILE LYS LEU VAL LYS THR GLU LEU GLN SER PRO SEQRES 12 B 368 GLU HIS PRO LEU ASP GLN HIS TYR ARG ASN LEU HIS CYS SEQRES 13 B 368 ALA LEU ARG PRO LEU ASP HIS GLU SER TYR GLU PHE LYS SEQRES 14 B 368 VAL ILE SER GLN TYR LEU GLN SER THR HIS ALA PRO THR SEQRES 15 B 368 HIS SER ASP TYR THR MET THR LEU LEU ASP LEU PHE GLU SEQRES 16 B 368 VAL GLU LYS ASP GLY GLU LYS GLU ALA PHE ARG GLU ASP SEQRES 17 B 368 LEU HIS ASN ARG MET LEU LEU TRP HIS GLY SER ARG MET SEQRES 18 B 368 SER ASN TRP VAL GLY ILE LEU SER HIS GLY LEU ARG ILE SEQRES 19 B 368 ALA HIS PRO GLU ALA PRO ILE THR GLY TYR MET PHE GLY SEQRES 20 B 368 LYS GLY ILE TYR PHE ALA ASP MET SER SER LYS SER ALA SEQRES 21 B 368 ASN TYR CYS PHE ALA SER ARG LEU LYS ASN THR GLY LEU SEQRES 22 B 368 LEU LEU LEU SER GLU VAL ALA LEU GLY GLN CYS ASN GLU SEQRES 23 B 368 LEU LEU GLU ALA ASN PRO LYS ALA GLU GLY LEU LEU GLN SEQRES 24 B 368 GLY LYS HIS SER THR LYS GLY LEU GLY LYS MET ALA PRO SEQRES 25 B 368 SER SER ALA HIS PHE VAL THR LEU ASN GLY SER THR VAL SEQRES 26 B 368 PRO LEU GLY PRO ALA SER ASP THR GLY ILE LEU ASN PRO SEQRES 27 B 368 ASP GLY TYR THR LEU ASN TYR ASN GLU TYR ILE VAL TYR SEQRES 28 B 368 ASN PRO ASN GLN VAL ARG MET ARG TYR LEU LEU LYS VAL SEQRES 29 B 368 GLN PHE ASN PHE HET 78P A 1 18 HET GOL A 580 6 HET 78P B 1 18 HET GOL B 2 6 HETNAM 78P (2R)-2-(7-CARBAMOYL-1H-BENZIMIDAZOL-2-YL)-2- HETNAM 2 78P METHYLPYRROLIDINIUM HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 78P 2(C13 H16 N4 O) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 7 HOH *490(H2 O) HELIX 1 1 THR A 226 GLN A 232 1 7 HELIX 2 2 ASP A 235 CYS A 246 1 12 HELIX 3 3 ASN A 247 MET A 258 1 12 HELIX 4 4 PRO A 266 LEU A 270 5 5 HELIX 5 5 THR A 271 ALA A 291 1 21 HELIX 6 6 GLY A 295 ILE A 309 1 15 HELIX 7 7 THR A 323 LYS A 348 1 26 HELIX 8 8 HIS A 356 LEU A 365 1 10 HELIX 9 9 SER A 376 THR A 389 1 14 HELIX 10 10 GLY A 411 PHE A 416 1 6 HELIX 11 11 ARG A 431 SER A 433 5 3 HELIX 12 12 ASN A 434 GLY A 442 1 9 HELIX 13 13 PRO A 451 TYR A 455 5 5 HELIX 14 14 MET A 466 TYR A 473 1 8 HELIX 15 15 LYS A 504 LEU A 509 5 6 HELIX 16 16 SER A 525 PHE A 528 5 4 HELIX 17 17 ASN A 563 ASN A 565 5 3 HELIX 18 18 ASP B 223 GLN B 232 1 10 HELIX 19 19 ASP B 235 CYS B 246 1 12 HELIX 20 20 ASN B 247 MET B 258 1 12 HELIX 21 21 PRO B 266 LEU B 270 5 5 HELIX 22 22 THR B 271 ALA B 291 1 21 HELIX 23 23 GLY B 295 ILE B 309 1 15 HELIX 24 24 THR B 323 VAL B 347 1 25 HELIX 25 25 HIS B 356 HIS B 366 1 11 HELIX 26 26 SER B 376 THR B 389 1 14 HELIX 27 27 GLY B 411 PHE B 416 1 6 HELIX 28 28 ARG B 431 SER B 433 5 3 HELIX 29 29 ASN B 434 GLY B 442 1 9 HELIX 30 30 PRO B 451 TYR B 455 5 5 HELIX 31 31 MET B 466 TYR B 473 1 8 HELIX 32 32 LYS B 504 LEU B 509 5 6 HELIX 33 33 SER B 525 PHE B 528 5 4 HELIX 34 34 ASN B 563 ASN B 565 5 3 SHEET 1 A 5 CYS A 367 PRO A 371 0 SHEET 2 A 5 THR A 398 LYS A 409 -1 O GLU A 406 N ARG A 370 SHEET 3 A 5 VAL A 567 ASN A 578 -1 O ASN A 578 N THR A 398 SHEET 4 A 5 THR A 482 ALA A 491 -1 N LEU A 485 O LEU A 573 SHEET 5 A 5 ARG A 423 GLY A 429 -1 N MET A 424 O VAL A 490 SHEET 1 B 4 ILE A 461 PHE A 463 0 SHEET 2 B 4 GLU A 558 VAL A 561 -1 O VAL A 561 N ILE A 461 SHEET 3 B 4 SER A 514 GLY A 517 -1 N THR A 515 O ILE A 560 SHEET 4 B 4 CYS A 495 LEU A 498 1 N ASN A 496 O SER A 514 SHEET 1 C 3 ALA A 541 ASP A 543 0 SHEET 2 C 3 GLY A 519 PRO A 523 -1 N ALA A 522 O SER A 542 SHEET 3 C 3 LEU A 554 TYR A 556 1 O LEU A 554 N LYS A 520 SHEET 1 D 2 VAL A 529 LEU A 531 0 SHEET 2 D 2 SER A 534 VAL A 536 -1 O VAL A 536 N VAL A 529 SHEET 1 E 5 CYS B 367 PRO B 371 0 SHEET 2 E 5 THR B 398 LYS B 409 -1 O GLU B 408 N ALA B 368 SHEET 3 E 5 VAL B 567 ASN B 578 -1 O ASN B 578 N THR B 398 SHEET 4 E 5 THR B 482 ALA B 491 -1 N GLY B 483 O VAL B 575 SHEET 5 E 5 ARG B 423 GLY B 429 -1 N HIS B 428 O LEU B 486 SHEET 1 F 4 ILE B 461 PHE B 463 0 SHEET 2 F 4 GLU B 558 VAL B 561 -1 O VAL B 561 N ILE B 461 SHEET 3 F 4 SER B 514 GLY B 517 -1 N GLY B 517 O GLU B 558 SHEET 4 F 4 CYS B 495 LEU B 498 1 N ASN B 496 O SER B 514 SHEET 1 G 3 ALA B 541 ASP B 543 0 SHEET 2 G 3 GLY B 519 PRO B 523 -1 N ALA B 522 O SER B 542 SHEET 3 G 3 LEU B 554 TYR B 556 1 O LEU B 554 N LYS B 520 SHEET 1 H 2 VAL B 529 LEU B 531 0 SHEET 2 H 2 SER B 534 VAL B 536 -1 O VAL B 536 N VAL B 529 CISPEP 1 GLY A 539 PRO A 540 0 4.34 CISPEP 2 GLY B 539 PRO B 540 0 2.75 SITE 1 AC1 7 HOH A 161 HOH A 183 HIS A 428 GLY A 429 SITE 2 AC1 7 TYR A 462 SER A 470 TYR A 473 SITE 1 AC2 7 ASP A 396 ALA A 471 ASN A 472 CYS A 474 SITE 2 AC2 7 PHE A 475 ALA A 476 PHE A 577 SITE 1 AC3 7 HOH B 5 HIS B 428 GLY B 429 TYR B 462 SITE 2 AC3 7 SER B 470 TYR B 473 HOH B 584 SITE 1 AC4 8 ASP B 396 TYR B 397 ALA B 471 ASN B 472 SITE 2 AC4 8 PHE B 475 ALA B 476 HOH B 659 HOH B 710 CRYST1 58.134 134.611 58.314 90.00 117.68 90.00 P 1 21 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 0.017202 0.000000 0.009021 0.00000 SCALE2 0.000000 0.007429 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019364 0.00000