› 3nr6

X-ray diffraction
1.97Å resolution

Crystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease

Released:
DOI: 10.2210/pdb3nr6/pdb
PDB entry 3nr6 coloured by chain, front view.
PDB entry 3nr6 coloured by chain, side view.
PDB entry 3nr6 coloured by chain, top view.
Source organism: Xenotropic MuLV-related virus VP62
Primary publication:
Crystal structure of XMRV protease differs from the structures of other retropepsins.
Li M, Dimaio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A
Nat Struct Mol Biol 18 227-9 (2011)
PMID: 21258323

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-106769 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protease p14 Chains: A, B
Molecule details ›
Chains: A, B
Length: 132 amino acids
Theoretical weight: 14.35 KDa
Source organism: Xenotropic MuLV-related virus VP62
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1Z651 (Residues: 533-657; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

2 bound ligands:
Ligand K 1 x K
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P422
Unit cell:
a: 63.915Å b: 63.915Å c: 106.509Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.233
Expression system: Escherichia coli BL21(DE3)

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Citations

2 review citations

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.
Adams et al. (2013)
1 more

11 mentions without citation

Ddi1-like protein from Leishmania major is an active aspartyl proteinase.
Perteguer et al. (2013)
10 more