› 1sp5

X-ray diffraction
1.8Å resolution

Crystal structure of HIV-1 protease complexed with a product of autoproteolysis

Released:
DOI: 10.2210/pdb1sp5/pdb
PDB entry 1sp5 coloured by chain, front view.
PDB entry 1sp5 coloured by chain, side view.
PDB entry 1sp5 coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Entry authors: Vondrackova E, Hasek J, Jaskolski M, Rezacova P, Dohnalek J, Skalova T, Petrokova H, Duskova J, Brynda J, Sedlacek J

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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136857 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.8 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
Protease Chain: I
Molecule details ›
Chain: I
Length: 5 amino acids
Theoretical weight: 651 Da
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P03367 (Residues: 559-563; Coverage: 0%)
Gene name: gag-pol

Ligands and Environments

3 bound ligands:
Ligand CL 3 x CL
Ligand BME 3 x BME
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P21212
Unit cell:
a: 57.765Å b: 86.284Å c: 45.834Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.177 0.211
Expression system: Escherichia coli BL21(DE3)

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