PDBe 3hpg

X-ray diffraction
3.28Å resolution

Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces


Function and Biology Details

Reactions catalysed:
Endonucleolytic cleavage to 5'-phosphomonoester.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
dUTP + H(2)O = dUMP + diphosphate
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Integrase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 219 amino acids
Theoretical weight: 25.09 KDa
Source organism: Visna/maedi virus EV1 KV1772
Expression system: Escherichia coli
  • Canonical: P35956 (Residues: 1228-1444; Coverage: 14%)
Gene name: pol
Sequence domains:
Structure domains:
PC4 and SFRS1-interacting protein Chains: G, H, I, J, K, L
Molecule details ›
Chains: G, H, I, J, K, L
Length: 95 amino acids
Theoretical weight: 11.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: O75475 (Residues: 347-435; Coverage: 17%)
Gene names: DFS70, LEDGF, PSIP1, PSIP2
Structure domains: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 91.104Å b: 148.904Å c: 91.076Å
α: 90° β: 113.41° γ: 90°
R R work R free
0.214 0.212 0.253
Expression system: Escherichia coli