› 8buv

X-ray diffraction
2.04Å resolution

HIV-1 Integrase Catalytic Core Domain and C-Terminal Domain in Complex with Allosteric Integrase Inhibitor LEDGIN 3

Released:
DOI: 10.2210/pdb8buv/pdb
PDB entry 8buv coloured by chain, front view.
PDB entry 8buv coloured by chain, side view.
PDB entry 8buv coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Entry authors: Singer MR, Pye VE, Cook NJ, Cherepanov P

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146235 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Integrase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 233 amino acids
Theoretical weight: 25.9 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12497 (Residues: 1188-1190, 1191-1359; Coverage: 12%)
Gene name: gag-pol
Sequence domains: Integrase core domain

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand EDO 6 x EDO
Ligand 723 2 x 723
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 53.84Å b: 65.16Å c: 69.79Å
α: 90° β: 99.9° γ: 90°
R-values:
R R work R free
0.217 0.215 0.247
Expression system: Escherichia coli BL21(DE3)

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