Structure of PDB 1rc8 Chain A Binding Site BS03

Receptor Information
>1rc8 Chain A (length=289) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEY
KYTKKKEGIVTGMQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFA
KEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLP
VYNGTPGKPKAVIFDVDGTLAKMTDVINPMVVELSKMYALMGYQIVVVSG
RESGTKEDPTKYYRMTRKWVEDIAGVPLVMQCQREQGDTRKDDVVKEEIF
WKHIAPHFDVKLAIDDRTQVVEMWRRIGVECWQVASGDF
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 chain1rc8 Chain A Residue 900 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rc8 Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		G12 G14 K15 S16 T17
Binding residue
(residue number reindexed from 1)		G12 G14 K15 S16 T17
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K15 D35 R126 D165
Catalytic site (residue number reindexed from 1) K15 D35 R126 D165
Enzyme Commision number 2.7.1.78: polynucleotide 5'-hydroxyl-kinase.
3.1.3.34: deoxynucleotide 3'-phosphatase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016787 hydrolase activity
GO:0046404 ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity
GO:0047846 deoxynucleotide 3'-phosphatase activity
GO:0051734 ATP-dependent polynucleotide 5'-hydroxyl-kinase activity
Biological Process
GO:0006281 DNA repair
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1rc8, PDBe:1rc8, PDBj:1rc8
PDBsum1rc8
PubMed14754987
UniProtP06855|KIPN_BPT4 Polynucleotide kinase (Gene Name=pseT)

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