Structure of PDB 3zvn Chain A Binding Site BS05

Receptor Information
>3zvn Chain A (length=377) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
WESLKKLLVFTASGVKPQGKVAAFNLDGTLITTRSGKVFPTSPSDWRILY
PEIPKKLQELAAEGYKLVIFTNQMGIGRGKLPAEVFKGKVEAVLEKLGVP
FQVLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGRLAN
WAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAARFELPAFDPRTI
SSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVNR
DTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGVPCR
CFNFCATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPPTLAEGFL
EILEIPFRLQEHLDPALQRLYRQFSEG
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain3zvn Chain A Residue 1524 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3zvn The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G374 G376 K377 S378 T379 N459 R463 F502 R503 L504 Q505
Binding residue
(residue number reindexed from 1)		G229 G231 K232 S233 T234 N314 R318 F357 R358 L359 Q360
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.78: polynucleotide 5'-hydroxyl-kinase.
3.1.3.32: polynucleotide 3'-phosphatase.
Gene Ontology
Molecular Function
GO:0046403 polynucleotide 3'-phosphatase activity
GO:0046404 ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
Biological Process
GO:0006281 DNA repair

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Molecular Function
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Biological Process
External links
PDB RCSB:3zvn, PDBe:3zvn, PDBj:3zvn
PDBsum3zvn
PubMed22055185
UniProtQ9JLV6|PNKP_MOUSE Bifunctional polynucleotide phosphatase/kinase (Gene Name=Pnkp)

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