› 4rbm

X-ray diffraction
1.75Å resolution

Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like domains

Released:
DOI: 10.2210/pdb4rbm/pdb
PDB entry 4rbm coloured by chain, front view.
PDB entry 4rbm coloured by chain, side view.
PDB entry 4rbm coloured by chain, top view.
Source organism: Porphyromonas gingivalis
Primary publication:
Structure and mechanism of cysteine peptidase gingipain K (Kgp), a major virulence factor of Porphyromonas gingivalis in periodontitis.
de Diego I, Veillard F, Sztukowska MN, Guevara T, Potempa B, Pomowski A, Huntington JA, Potempa J, Gomis-Rüth FX
J Biol Chem 289 32291-32302 (2014)
PMID: 25266723

Function and Biology Details

Reaction catalysed: 
Endopeptidase with strict specificity for lysyl bonds.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-175977 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lys-gingipain catalytic subunit Chain: A
Molecule details ›
Chain: A
Length: 461 amino acids
Theoretical weight: 51.01 KDa
Source organism: Porphyromonas gingivalis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q51817 (Residues: 229-683; Coverage: 27%)
Gene names: kgp, prtK, prtP
Sequence domains:

Ligands and Environments

8 bound ligands:
Ligand CA 2 x CA
Ligand NA 3 x NA
Ligand NI 1 x NI
Ligand HIS 1 x HIS
Ligand ACT 2 x ACT
Ligand AZI 3 x AZI
Ligand GOL 4 x GOL
Ligand CKC 1 x CKC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 56.64Å b: 58.81Å c: 135.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.15 0.149 0.172
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line.
How et al. (2016)
9 more

8 mentions without citation

Structure and mechanism of cysteine peptidase gingipain K (Kgp), a major virulence factor of Porphyromonas gingivalis in periodontitis.
de Diego et al. (2014)
7 more