› 4bdy

X-ray diffraction
2.52Å resolution

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117252 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 395 amino acids
Theoretical weight: 44.46 KDa
Source organism: Human spumaretrovirus
Expression system: Escherichia coli
UniProt:
  • Canonical: P14350 (Residues: 752-1143; Coverage: 34%)
Gene name: pol
Sequence domains:
Structure domains:
19 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND) Chain: C
Molecule details ›
Chain: C
Length: 19 nucleotides
Theoretical weight: 5.83 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided
17 NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND) Chain: D
Molecule details ›
Chain: D
Length: 17 nucleotides
Theoretical weight: 5.2 KDa
Source organism: Human spumaretrovirus
Expression system: Not provided

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand SO4 3 x SO4
Ligand GOL 5 x GOL
Ligand MG 2 x MG
Ligand CIJ 1 x CIJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P41212
Unit cell:
a: 159.41Å b: 159.41Å c: 124.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.187 0.218
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Targeting Metalloenzymes for Therapeutic Intervention.
Chen et al. (2019)
6 more

1 mention without citation

Activities, crystal structures, and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase.
Métifiot et al. (2013)