Structure of PDB 3f9k Chain V Binding Site BS01

Receptor Information

>3f9k Chain V (length=196) Species: 11720 (Human immunodeficiency virus type 2 (ISOLATE ROD))

VLEKIEPAQEEHEKYHSNVKELSHKFGIPNLVARQIVNSCAQCVNAELGT
WQMDCTHLEGKIIIVAVHVASGFIEAEVIPQESGRQTALFLLKLASRWPI
THLHTDNGANFTSQEVKMVAWWIGIEQSFGVPYNPQSQGVVEAMNHHLKN
QISRIREQANTIETIVLMAVHCMNFKRRGGIGDMTPSERLINMITT

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 3f9k Chain V Residue 210

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3f9k A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): H12 H16 C40 C43
• Binding residue (residue number reindexed from 1): H12 H16 C40 C43
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.47: HIV-2 retropepsin.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:3f9k, PDBe:3f9k, PDBj:3f9k
• PDBsum: 3f9k
• PubMed: 19132083
• UniProt: P04584|POL_HV2RO Gag-Pol polyprotein (Gene Name=gag-pol)