Structure of PDB 3zvm Chain A Binding Site BS02

Receptor Information
>3zvm Chain A (length=380) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLGWESLKKLLVFTASGVKPQGKVAAFDLDGTLITTRSGKVFPTSPSDWR
ILYPEIPKKLQELAAEGYKLVIFTNQMGIGRGKLPAEVFKGKVEAVLEKL
GVPFQVLVATHAGLNRKPVSGMWDHLQEQANEGIPISVEDSVFVGDAAGR
LANWAPGRKKKDFSCADRLFALNVGLPFATPEEFFLKWPAARFELPAFDP
RTISSAGPLYLPESSSLLSPNPEVVVAVGFPGAGKSTFIQEHLVSAGYVH
VNRDTLGSWQRCVSSCQAALRQGKRVVIDNTNPDVPSRARYIQCAKDAGV
PCRCFNFCATIEQARHNNRFREMTDPSHAPVSDMVMFSYRKQFEPPTLAE
GFLEILEIPFRLQEHLDPALQRLYRQFSEG
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 chain3zvm Chain A Residue 1523 [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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PDB3zvm The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase.
Resolution1.997 Å
Binding residue
(original residue number in PDB)		G374 G376 K377 S378 T379 N459 R463 F502 L504 Q505
Binding residue
(residue number reindexed from 1)		G232 G234 K235 S236 T237 N317 R321 F360 L362 Q363
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:3zvm, PDBe:3zvm, PDBj:3zvm
PDBsum3zvm
PubMed22055185
UniProtQ9JLV6|PNKP_MOUSE Bifunctional polynucleotide phosphatase/kinase (Gene Name=Pnkp)

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