Structure of PDB 2b9s Chain A Binding Site BS04

Receptor Information

>2b9s Chain A (length=426) Species: 5661 (Leishmania donovani)

DLNWWEQENLRIAMKGERRWETLAHNGVLFPPEYEPHGIPIFYDGREFKM
TPEEEEVATMFAVMKEHDYYRMEVFRRNFFESWREILDKRQHPIRRLELC
DFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYRYCVWDGRREQV
ANFRVEPPGLFRGRGKHPLMGKLKVRVQPEDITINIGETAEVPVPPAGHK
WAAVQHDHTVTWLAMWRDSVAGNMKYVMLAPSSSVKGQSDMVKFEKARKL
KDKVDDIRASYMEDFKSNDLHVAQRAVAMYFIDRLALRVGNEKGEDEADT
VGCCSLRVEHIQLMPDNIVRFDFLGKDSIRYQNDVAVLPEVYALLQRFTR
RKSPGMDIFDQLNPTQLNDHLKSFMDGLSAKVFRTYNASITLDRWFKEKP
WSTADKLAYFNKANTEVAILCNHQKS

Ligand information

• Ligand ID: VO4
• InChI: InChI=1S/4O.V/q;3*-1;
• InChIKey: LSGOVYNHVSXFFJ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341: [O-][V]([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-][V](=O)([O-])[O-]
• Formula: O4 V
• Name: VANADATE ION
• PDB chain: 2b9s Chain B Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2b9s The Structure of the Transition State of the Heterodimeric Topoisomerase I of Leishmania donovani as a Vanadate Complex with Nicked DNA.
• Resolution: 2.27 Å
• Binding residue (original residue number in PDB): R314 R410 H453
• Binding residue (residue number reindexed from 1): R288 R384 H423
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.6.2.1: DNA topoisomerase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity

Biological Process

• GO:0006265 DNA topological change

Cellular Component

• GO:0005694 chromosome

External links

• PDB: RCSB:2b9s, PDBe:2b9s, PDBj:2b9s
• PDBsum: 2b9s
• PubMed: 16487540
• UniProt: Q9GPZ9