› 3nxe

X-ray diffraction
1.61Å resolution

X-ray structure of ester chemical analogue 'covalent dimer' [Ile50,O-Ile50']HIV-1 protease complexed with MVT-101 inhibitor

Released:
DOI: 10.2210/pdb3nxe/pdb
PDB entry 3nxe coloured by chain, front view.
PDB entry 3nxe coloured by chain, side view.
PDB entry 3nxe coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Torbeev VY, Raghuraman H, Hamelberg D, Tonelli M, Westler WM, Perozo E, Kent SB
Proc Natl Acad Sci U S A 108 20982-7 (2011)
PMID: 22158985

Function and Biology Details

Reaction catalysed: 
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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128758 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase A2 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 203 amino acids
Theoretical weight: 21.89 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: O38716 (Residues: 1-99; Coverage: 100%)
Gene name: pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

2 bound ligands:
Ligand 2NC 1 x 2NC
Ligand SO4 4 x SO4
3 modified residues:
Ligand NLE 4 x NLE
Ligand YCM 3 x YCM
Ligand ABA 4 x ABA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 51.566Å b: 57.78Å c: 61.591Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.185 0.22
Expression system: Not provided

Quick links

Citations

9 review citations

Expanding the chemical toolbox for the synthesis of large and uniquely modified proteins.
Bondalapati et al. (2016)
8 more

1 mention without citation

Protein conformational dynamics in the mechanism of HIV-1 protease catalysis.
Torbeev et al. (2011)