Structure of PDB 6v3k Chain B Binding Site BS01

Receptor Information

>6v3k Chain B (length=242) Species: 11698,273057

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCSPGIWQL
DCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTV
HTDNGSNFTSTTVKAACWWAGIKQEFGVIESMNKELKKIIGQVRDQAEHL
KTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQN
FRVYYRWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRD

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: 6v3k Chain B Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6v3k Structural basis for strand-transfer inhibitor binding to HIV intasomes.
• Resolution: 3.4 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.
  3.4.23.16: HIV-1 retropepsin.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0004521 RNA endonuclease activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:6v3k, PDBe:6v3k, PDBj:6v3k
• PDBsum: 6v3k
• PubMed: 32001521
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol);
  P39476|DN7D_SACS2 DNA-binding protein 7d (Gene Name=sso7d)