Structure of PDB 1d3y Chain B Binding Site BS01

Receptor Information

>1d3y Chain B (length=290) Species: 2190 (Methanocaldococcus jannaschii)

NQAKIFAQTTKMLEFAKQLLETDDFSTLREAYYVSKNWGEARFDDQQASN
NVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGELVVDCTKL
GTGAYNIPNDVTKLNLETDADFILAIETSGMFARLNAERFWDKHNCILVS
LKGVPARATRRFIKRLHEEHDLPVLVFTDGDPYGYLNIYRTLKVGKLSIP
AARLIGVTPQDIIDYDLPTHPLKEQDIKRIKDGLKNDDFVRSFPEWQKAL
KQMLDMGVRAEQQSLAKYGLKYVVNTYLPEKIKDESTWLP

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 1d3y Chain B Residue 374

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1d3y Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): E197 D249
• Binding residue (residue number reindexed from 1): E127 D179
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006265 DNA topological change

Cellular Component

• GO:0005694 chromosome

External links

• PDB: RCSB:1d3y, PDBe:1d3y, PDBj:1d3y
• PDBsum: 1d3y
• PubMed: 10545127
• UniProt: Q57815|TOP6A_METJA Type 2 DNA topoisomerase 6 subunit A (Gene Name=top6A)