PDBe 3hph

X-ray diffraction
2.64Å resolution

Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD


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
Molecule details ›
Chains: A, B, C, D
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: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 94 amino acids
Theoretical weight: 10.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: O75475 (Residues: 348-435; Coverage: 17%)
Gene names: DFS70, LEDGF, PSIP1, PSIP2
Structure domains: Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Ligands and Environments

3 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 102.87Å b: 83.15Å c: 115.3Å
α: 90° β: 101.96° γ: 90°
R R work R free
0.228 0.226 0.253
Expression system: Escherichia coli