PDBe 5eu7

X-ray diffraction
2.64Å resolution

Crystal structure of HIV-1 integrase catalytic core in complex with Fab


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:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Integrase Chains: A, B
Molecule details ›
Chains: A, B
Length: 153 amino acids
Theoretical weight: 16.71 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
  • Canonical: P04585 (Residues: 1204-1356; Coverage: 11%)
Gene name: gag-pol
FAB Heavy Chain Chains: E, F
Molecule details ›
Chains: E, F
Length: 233 amino acids
Theoretical weight: 24.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
FAB light chain Chains: C, D
Molecule details ›
Chains: C, D
Length: 214 amino acids
Theoretical weight: 23.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P21
Unit cell:
a: 82.489Å b: 87.65Å c: 96.339Å
α: 90° β: 95.83° γ: 90°
R R work R free
0.184 0.181 0.233
Expression system: Escherichia coli BL21(DE3)