PDBe 4q5m

X-ray diffraction
1.8Å resolution

D30N tethered HIV-1 protease dimer/saquinavir complex

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
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protease Chain: A
Molecule details ›
Chain: A
Length: 203 amino acids
Theoretical weight: 21.9 KDa
Source organism: HIV-1 M:B_HXB2R
Expression system: Escherichia coli
UniProt:
  • Canonical: P04585 (Residues: 489-587; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P61
Unit cell:
a: 62.84Å b: 62.84Å c: 82.49Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.206 0.235
Expression system: Escherichia coli