PDBe 3ao2

X-ray diffraction
1.8Å resolution

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

Released:

Function and Biology Details

Reactions catalysed:
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. 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). 
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. 
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid. 
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 163 amino acids
Theoretical weight: 17.77 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 1197-1359; Coverage: 11%)
Gene name: gag-pol
Sequence domains: Integrase core domain
Structure domains: Nucleotidyltransferase; domain 5

Ligands and Environments


No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P32
Unit cell:
a: 49.16Å b: 49.16Å c: 103.12Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.189 0.187 0.217
Expression system: Escherichia coli