› 1cvr

X-ray diffraction
2Å resolution

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Released:
DOI: 10.2210/pdb1cvr/pdb
PDB entry 1cvr coloured by chain, front view.
PDB entry 1cvr coloured by chain, side view.
PDB entry 1cvr coloured by chain, top view.
Source organism: Porphyromonas gingivalis
Primary publication:
Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold.
Eichinger A, Beisel HG, Jacob U, Huber R, Medrano FJ, Banbula A, Potempa J, Travis J, Bode W
EMBO J 18 5453-62 (1999)
PMID: 10523290

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins and small molecule substrates, with a preference for Arg in P1.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161161 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Gingipain R2 Chain: A
Molecule details ›
Chain: A
Length: 435 amino acids
Theoretical weight: 47.93 KDa
Source organism: Porphyromonas gingivalis
Expression system: Not provided
UniProt:
  • Canonical: P95493 (Residues: 230-664; Coverage: 61%)
Gene names: PG_0506, prtRII, rgp2, rgpB
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand H37 1 x H37
Ligand CA 6 x CA
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 51.93Å b: 79.92Å c: 99.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.163 0.207
Expression system: Not provided

Quick links

Citations

26 review citations

The protein structures that shape caspase activity, specificity, activation and inhibition.
Fuentes-Prior et al. (2004)
25 more

25 mentions without citation

Comparative structural analysis of the caspase family with other clan CD cysteine peptidases.
McLuskey et al. (2015)
24 more