› 1rl8

X-ray diffraction
2Å resolution

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Released:
DOI: 10.2210/pdb1rl8/pdb
PDB entry 1rl8 coloured by chain, front view.
PDB entry 1rl8 coloured by chain, side view.
PDB entry 1rl8 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Entry authors: Rezacova P, Brynda J, Sedlacek J, Konvalinka J, Fabry M, Horejsi M

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
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136860 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.69 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P03367 (Residues: 501-599; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

1 bound ligand:
Ligand RIT 1 x RIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE X13
Spacegroup: P61
Unit cell:
a: 61.414Å b: 61.414Å c: 80.816Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.226 0.269
Expression system: Escherichia coli BL21(DE3)

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