6t6j

X-ray diffraction
2Å resolution

Crystal Structure of the C-terminal domain of the HIV-1 Integrase (subtype A2, mutant N254K, K340Q)

Released:
Model geometry
Fit model/data

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:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181098 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Integrase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 59 amino acids
Theoretical weight: 7.05 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q75002 (Residues: 1370-1421; Coverage: 4%)
Gene name: gag-pol
Sequence domains: Integrase DNA binding domain

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06DA
Spacegroup: C2
Unit cell:
a: 85.306Å b: 48.835Å c: 66.749Å
α: 90° β: 110.37° γ: 90°
R-values:
R R work R free
0.172 0.166 0.22
Expression system: Escherichia coli