› 3ndu

X-ray diffraction
1.25Å resolution

HIV-1 Protease Saquinavir:Ritonavir 1:5 complex structure

Released:
DOI: 10.2210/pdb3ndu/pdb
PDB entry 3ndu coloured by chain, front view.
PDB entry 3ndu coloured by chain, side view.
PDB entry 3ndu coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures
Olajuyigbe FM, Demitri N, Geremia S
Cryst Growth Des 11 4378-4385 (2011)

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, C, D
Molecule details ›
Chains: A, B, C, D
Length: 100 amino acids
Theoretical weight: 10.77 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03367 (Residues: 501-599; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

6 bound ligands:
Ligand ROC 2 x ROC
Ligand DMS 5 x DMS
Ligand ACT 4 x ACT
Ligand CL 6 x CL
Ligand GOL 3 x GOL
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ELETTRA BEAMLINE 5.2R
Spacegroup: P21
Unit cell:
a: 51.19Å b: 62.705Å c: 59.296Å
α: 90° β: 98.32° γ: 90°
R-values:
R R work R free
0.142 0.13 0.194
Expression system: Escherichia coli

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