Structure of PDB 1rc8 Chain A Binding Site BS02

Receptor Information

>1rc8 Chain A (length=289) Species: 10665 (Tequatrovirus T4)

MKKIILTIGCPGSGKSTWAREFIAKNPGFYNINRDDYRQSIMAHEERDEY
KYTKKKEGIVTGMQFDTAKSILYGGDSVKGVIISDTNLNPERRLAWETFA
KEYGWKVEHKVFDVPWTELVKRNSKRGTKAVPIDVLRSMYKSMREYLGLP
VYNGTPGKPKAVIFDVDGTLAKMTDVINPMVVELSKMYALMGYQIVVVSG
RESGTKEDPTKYYRMTRKWVEDIAGVPLVMQCQREQGDTRKDDVVKEEIF
WKHIAPHFDVKLAIDDRTQVVEMWRRIGVECWQVASGDF

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 1rc8 Chain A Residue 700

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rc8 Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase.
• Resolution: 2.75 Å
• Binding residue (original residue number in PDB): D165 D167 D278
• Binding residue (residue number reindexed from 1): D165 D167 D266
• Annotation score: 1

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

External links

• PDB: RCSB:1rc8, PDBe:1rc8, PDBj:1rc8
• PDBsum: 1rc8
• PubMed: 14754987
• UniProt: P06855|KIPN_BPT4 Polynucleotide kinase (Gene Name=pseT)