HEADER HYDROLASE/TRANSFERASE 25-JUL-11 3ZVL TITLE THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN TITLE 2 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: POLYNUCLEOTIDE 3'-PHOSPHATASE AND POLYNUCLEOTIDE 5'- COMPND 5 HYDROXYL-KINASE DOMAINS, RESIDUES 111-522; COMPND 6 SYNONYM: DNA 5'-KINASE/3'-PHOSPHATASE, POLYNUCLEOTIDE KINASE-3'- COMPND 7 PHOSPHATASE, PNKP; COMPND 8 EC: 3.1.3.32, 2.7.1.78; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA2 (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PTWO-E KEYWDS HYDROLASE-TRANSFERASE COMPLEX, BASE EXCISION REPAIR, BER, NON- KEYWDS 2 HOMOLOGOUS END-JOINING, NHEJ, DNA REPAIR, CANCER EXPDTA X-RAY DIFFRACTION AUTHOR F.GARCES,L.H.PEARL,A.W.OLIVER REVDAT 2 20-DEC-23 3ZVL 1 REMARK LINK REVDAT 1 16-NOV-11 3ZVL 0 JRNL AUTH F.GARCES,L.H.PEARL,A.W.OLIVER JRNL TITL THE STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY MAMMALIAN JRNL TITL 2 POLYNUCLEOTIDE KINASE 3' PHOSPHATASE. JRNL REF MOL.CELL V. 44 385 2011 JRNL REFN ISSN 1097-2765 JRNL PMID 22055185 JRNL DOI 10.1016/J.MOLCEL.2011.08.036 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.840 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 76395 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3839 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.9400 - 3.5537 0.96 7803 416 0.1492 0.1753 REMARK 3 2 3.5537 - 2.8211 0.97 7890 427 0.1545 0.2155 REMARK 3 3 2.8211 - 2.4646 0.97 7909 421 0.1653 0.2189 REMARK 3 4 2.4646 - 2.2393 0.96 7870 397 0.1605 0.2120 REMARK 3 5 2.2393 - 2.0789 0.96 7859 431 0.1597 0.2310 REMARK 3 6 2.0789 - 1.9563 0.96 7779 420 0.1728 0.2172 REMARK 3 7 1.9563 - 1.8583 0.95 7746 413 0.1869 0.2622 REMARK 3 8 1.8583 - 1.7775 0.93 7553 414 0.2202 0.2674 REMARK 3 9 1.7775 - 1.7090 0.70 5720 280 0.2432 0.3027 REMARK 3 10 1.7090 - 1.6501 0.54 4427 220 0.2554 0.2935 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.94670 REMARK 3 B22 (A**2) : 3.52240 REMARK 3 B33 (A**2) : -2.57570 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.62740 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3099 REMARK 3 ANGLE : 1.026 4217 REMARK 3 CHIRALITY : 0.069 458 REMARK 3 PLANARITY : 0.005 557 REMARK 3 DIHEDRAL : 15.992 1137 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ZVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUL-11. REMARK 100 THE DEPOSITION ID IS D_1290049158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39354 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 33.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: PDB ENTRY 1YJ5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M NACACODYLATE PH 6.5, 0.2 M REMARK 280 AMMONIUM ACETATE, 0.01 M MG ACETATE, 30 % (W/V) PEG 8000. 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 31.75000 REMARK 290 SMTRY3 2 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: 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 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 107 REMARK 465 PRO A 108 REMARK 465 HIS A 109 REMARK 465 MET A 110 REMARK 465 THR A 111 REMARK 465 SER A 112 REMARK 465 GLY A 113 REMARK 465 SER A 114 REMARK 465 GLN A 115 REMARK 465 PRO A 116 REMARK 465 ASP A 117 REMARK 465 ALA A 118 REMARK 465 PRO A 119 REMARK 465 PRO A 120 REMARK 465 ASP A 121 REMARK 465 THR A 122 REMARK 465 PRO A 123 REMARK 465 GLY A 124 REMARK 465 ASP A 125 REMARK 465 PRO A 126 REMARK 465 GLU A 127 REMARK 465 GLU A 128 REMARK 465 GLY A 129 REMARK 465 GLU A 130 REMARK 465 ASP A 131 REMARK 465 THR A 132 REMARK 465 GLU A 133 REMARK 465 PRO A 134 REMARK 465 GLN A 135 REMARK 465 LYS A 136 REMARK 465 LYS A 137 REMARK 465 ARG A 138 REMARK 465 VAL A 139 REMARK 465 ARG A 140 REMARK 465 LYS A 141 REMARK 465 SER A 142 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 LYS A 150 CG CD CE NZ REMARK 470 LYS A 302 CG CD CE NZ REMARK 470 GLU A 336 CG CD OE1 OE2 REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 398 CG CD1 CD2 REMARK 470 GLN A 402 CG CD OE1 NE2 REMARK 470 ARG A 403 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 438 CG CD CE NZ REMARK 470 LYS A 483 CG CD CE NZ REMARK 470 GLN A 505 CG CD OE1 NE2 REMARK 470 GLU A 506 CG CD OE1 OE2 REMARK 470 HIS A 507 CG ND1 CD2 CE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 223 NE CZ NH1 NH2 REMARK 480 LYS A 303 CE NZ 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 LEU A 171 -69.97 -96.82 REMARK 500 THR A 174 -53.27 -122.62 REMARK 500 PRO A 298 111.12 -36.55 REMARK 500 LYS A 301 5.21 -65.81 REMARK 500 ASP A 421 79.41 -114.34 REMARK 500 ASN A 424 66.77 -118.85 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 A2169 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2210 DISTANCE = 6.23 ANGSTROMS 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 A1524 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 170 OD2 REMARK 620 2 ASP A 172 O 89.8 REMARK 620 3 ASP A 288 OD1 86.6 94.0 REMARK 620 4 HOH A2033 O 102.2 92.6 169.0 REMARK 620 5 HOH A2034 O 87.5 174.7 90.3 83.6 REMARK 620 6 HOH A2036 O 175.0 88.4 88.8 82.5 94.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1523 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1524 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1525 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1526 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1527 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1528 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1529 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1530 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1531 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1532 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1533 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1534 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1535 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1536 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1537 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UJX RELATED DB: PDB REMARK 900 THE FORKHEAD ASSOCIATED (FHA) DOMAIN LIKE STRUCTURE FROMMOUSE REMARK 900 POLYNUCLEOTIDE KINASE 3'-PHOSPHATASE REMARK 900 RELATED ID: 1YJ5 RELATED DB: PDB REMARK 900 MOLECULAR ARCHITECTURE OF MAMMALIAN POLYNUCLEOTIDE KINASE, A DNA REMARK 900 REPAIR ENZYME REMARK 900 RELATED ID: 1YJM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FHA DOMAIN OF MOUSE POLYNUCLEOTIDEKINASE REMARK 900 IN COMPLEX WITH AN XRCC4-DERIVED PHOSPHOPEPTIDE. DBREF 3ZVL A 111 522 UNP Q9JLV6 PNKP_MOUSE 111 522 SEQADV 3ZVL GLY A 107 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVL PRO A 108 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVL HIS A 109 UNP Q9JLV6 EXPRESSION TAG SEQADV 3ZVL MET A 110 UNP Q9JLV6 EXPRESSION TAG SEQRES 1 A 416 GLY PRO HIS MET THR SER GLY SER GLN PRO ASP ALA PRO SEQRES 2 A 416 PRO ASP THR PRO GLY ASP PRO GLU GLU GLY GLU ASP THR SEQRES 3 A 416 GLU PRO GLN LYS LYS ARG VAL ARG LYS SER SER LEU GLY SEQRES 4 A 416 TRP GLU SER LEU LYS LYS LEU LEU VAL PHE THR ALA SER SEQRES 5 A 416 GLY VAL LYS PRO GLN GLY LYS VAL ALA ALA PHE ASP LEU SEQRES 6 A 416 ASP GLY THR LEU ILE THR THR ARG SER GLY LYS VAL PHE SEQRES 7 A 416 PRO THR SER PRO SER ASP TRP ARG ILE LEU TYR PRO GLU SEQRES 8 A 416 ILE PRO LYS LYS LEU GLN GLU LEU ALA ALA GLU GLY TYR SEQRES 9 A 416 LYS LEU VAL ILE PHE THR ASN GLN MET GLY ILE GLY ARG SEQRES 10 A 416 GLY LYS LEU PRO ALA GLU VAL PHE LYS GLY LYS VAL GLU SEQRES 11 A 416 ALA VAL LEU GLU LYS LEU GLY VAL PRO PHE GLN VAL LEU SEQRES 12 A 416 VAL ALA THR HIS ALA GLY LEU ASN ARG LYS PRO VAL SER SEQRES 13 A 416 GLY MET TRP ASP HIS LEU GLN GLU GLN ALA ASN GLU GLY SEQRES 14 A 416 ILE PRO ILE SER VAL GLU ASP SER VAL PHE VAL GLY ASP SEQRES 15 A 416 ALA ALA GLY ARG LEU ALA ASN TRP ALA PRO GLY ARG LYS SEQRES 16 A 416 LYS LYS ASP PHE SER CYS ALA ASP ARG LEU PHE ALA LEU SEQRES 17 A 416 ASN VAL GLY LEU PRO PHE ALA THR PRO GLU GLU PHE PHE SEQRES 18 A 416 LEU LYS TRP PRO ALA ALA ARG PHE GLU LEU PRO ALA PHE SEQRES 19 A 416 ASP PRO ARG THR ILE SER SER ALA GLY PRO LEU TYR LEU SEQRES 20 A 416 PRO GLU SER SER SER LEU LEU SER PRO ASN PRO GLU VAL SEQRES 21 A 416 VAL VAL ALA VAL GLY PHE PRO GLY ALA GLY LYS SER THR SEQRES 22 A 416 PHE ILE GLN GLU HIS LEU VAL SER ALA GLY TYR VAL HIS SEQRES 23 A 416 VAL ASN ARG ASP THR LEU GLY SER TRP GLN ARG CYS VAL SEQRES 24 A 416 SER SER CYS GLN ALA ALA LEU ARG GLN GLY LYS ARG VAL SEQRES 25 A 416 VAL ILE ASP ASN THR ASN PRO ASP VAL PRO SER ARG ALA SEQRES 26 A 416 ARG TYR ILE GLN CYS ALA LYS ASP ALA GLY VAL PRO CYS SEQRES 27 A 416 ARG CYS PHE ASN PHE CSX ALA THR ILE GLU GLN ALA ARG SEQRES 28 A 416 HIS ASN ASN ARG PHE ARG GLU MET THR ASP PRO SER HIS SEQRES 29 A 416 ALA PRO VAL SER ASP MET VAL MET PHE SER TYR ARG LYS SEQRES 30 A 416 GLN PHE GLU PRO PRO THR LEU ALA GLU GLY PHE LEU GLU SEQRES 31 A 416 ILE LEU GLU ILE PRO PHE ARG LEU GLN GLU HIS LEU ASP SEQRES 32 A 416 PRO ALA LEU GLN ARG LEU TYR ARG GLN PHE SER GLU GLY MODRES 3ZVL CSX A 450 CYS S-OXY CYSTEINE HET CSX A 450 7 HET GOL A1523 6 HET MG A1524 1 HET CL A1525 1 HET CL A1526 1 HET CL A1527 1 HET ACT A1528 4 HET ACT A1529 4 HET ACT A1530 4 HET ACT A1531 4 HET GOL A1532 6 HET GOL A1533 6 HET GOL A1534 6 HET GOL A1535 6 HET GOL A1536 6 HET CL A1537 1 HETNAM CSX S-OXY CYSTEINE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CSX C3 H7 N O3 S FORMUL 2 GOL 6(C3 H8 O3) FORMUL 3 MG MG 2+ FORMUL 4 CL 4(CL 1-) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 17 HOH *508(H2 O) HELIX 1 1 GLU A 197 GLU A 208 1 12 HELIX 2 2 GLN A 218 ARG A 223 1 6 HELIX 3 3 PRO A 227 GLY A 243 1 17 HELIX 4 4 SER A 262 ALA A 272 1 11 HELIX 5 5 SER A 279 SER A 283 5 5 HELIX 6 6 CYS A 307 GLY A 317 1 11 HELIX 7 7 THR A 322 LEU A 328 1 7 HELIX 8 8 ASP A 341 ILE A 345 5 5 HELIX 9 9 GLY A 376 LEU A 385 1 10 HELIX 10 10 VAL A 386 GLY A 389 5 4 HELIX 11 11 ASN A 394 LEU A 398 5 5 HELIX 12 12 SER A 400 GLN A 414 1 15 HELIX 13 13 ASP A 426 GLY A 441 1 16 HELIX 14 14 THR A 452 ASP A 467 1 16 HELIX 15 15 SER A 474 PHE A 485 1 12 HELIX 16 16 THR A 489 GLY A 493 5 5 HELIX 17 17 ASP A 509 ARG A 517 1 9 SHEET 1 AA 7 GLY A 145 LEU A 149 0 SHEET 2 AA 7 LEU A 152 THR A 156 -1 O LEU A 152 N LEU A 149 SHEET 3 AA 7 GLN A 247 ALA A 251 -1 O VAL A 248 N PHE A 155 SHEET 4 AA 7 LYS A 211 ASN A 217 1 O LEU A 212 N GLN A 247 SHEET 5 AA 7 VAL A 166 PHE A 169 1 O ALA A 167 N VAL A 213 SHEET 6 AA 7 VAL A 284 VAL A 286 1 O VAL A 284 N ALA A 168 SHEET 7 AA 7 PHE A 320 ALA A 321 1 N ALA A 321 O PHE A 285 SHEET 1 AB 2 ILE A 176 THR A 177 0 SHEET 2 AB 2 ARG A 192 ILE A 193 -1 O ARG A 192 N THR A 177 SHEET 1 AC 5 VAL A 391 HIS A 392 0 SHEET 2 AC 5 VAL A 418 ASP A 421 1 N VAL A 419 O VAL A 391 SHEET 3 AC 5 VAL A 366 VAL A 370 1 O VAL A 367 N ILE A 420 SHEET 4 AC 5 CYS A 444 PHE A 449 1 O ARG A 445 N VAL A 368 SHEET 5 AC 5 GLU A 496 ILE A 500 1 O GLU A 496 N CYS A 446 LINK C PHE A 449 N CSX A 450 1555 1555 1.33 LINK C CSX A 450 N ALA A 451 1555 1555 1.33 LINK OD2 ASP A 170 MG MG A1524 1555 1555 2.06 LINK O ASP A 172 MG MG A1524 1555 1555 2.08 LINK OD1 ASP A 288 MG MG A1524 1555 1555 2.19 LINK MG MG A1524 O HOH A2033 1555 1555 2.23 LINK MG MG A1524 O HOH A2034 1555 1555 2.21 LINK MG MG A1524 O HOH A2036 1555 1555 2.27 CISPEP 1 LYS A 259 PRO A 260 0 13.21 CISPEP 2 LEU A 353 PRO A 354 0 -0.15 SITE 1 AC1 6 ARG A 179 SER A 189 TRP A 191 ARG A 192 SITE 2 AC1 6 LYS A 241 HOH A2064 SITE 1 AC2 6 ASP A 170 ASP A 172 ASP A 288 HOH A2033 SITE 2 AC2 6 HOH A2034 HOH A2036 SITE 1 AC3 4 ASP A 170 ASN A 217 LYS A 259 HOH A2205 SITE 1 AC4 4 ASN A 217 GLN A 218 MET A 219 ARG A 258 SITE 1 AC5 4 PRO A 319 PHE A 320 GOL A1536 HOH A2209 SITE 1 AC6 3 ASN A 363 HOH A2363 HOH A2369 SITE 1 AC7 5 PRO A 185 SER A 187 PRO A 188 LYS A 234 SITE 2 AC7 5 HOH A2040 SITE 1 AC8 4 ALA A 375 PRO A 501 PHE A 502 ARG A 503 SITE 1 AC9 9 PHE A 372 PRO A 373 GLY A 374 ALA A 375 SITE 2 AC9 9 GLY A 376 LYS A 377 SER A 378 HOH A2374 SITE 3 AC9 9 HOH A2376 SITE 1 BC1 4 LYS A 201 TYR A 210 PHE A 326 GOL A1536 SITE 1 BC2 10 GLY A 159 VAL A 160 LYS A 161 GLN A 163 SITE 2 BC2 10 TYR A 210 LYS A 211 LEU A 212 HOH A2096 SITE 3 BC2 10 HOH A2112 HOH A2182 SITE 1 BC3 7 PRO A 338 HIS A 458 ARG A 461 PHE A 519 SITE 2 BC3 7 SER A 520 GLU A 521 HOH A2335 SITE 1 BC4 8 ASP A 172 ILE A 176 THR A 177 PRO A 185 SITE 2 BC4 8 ASP A 190 TRP A 191 LYS A 234 HOH A2042 SITE 1 BC5 5 PHE A 320 CL A1527 GOL A1532 HOH A2506 SITE 2 BC5 5 HOH A2507 SITE 1 BC6 2 LYS A 182 HOH A2390 CRYST1 42.750 63.500 67.900 90.00 91.82 90.00 P 1 21 1 2 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 0.023392 0.000000 0.000743 0.00000 SCALE2 0.000000 0.015748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014735 0.00000