› 3km5

X-ray diffraction
1.4Å resolution

Crystal Structure Analysis of the K2 Cleaved Adhesin Domain of Lys-gingipain (Kgp)

Released:
DOI: 10.2210/pdb3km5/pdb
PDB entry 3km5 coloured by chain, front view.
PDB entry 3km5 coloured by chain, side view.
PDB entry 3km5 coloured by chain, top view.
Source organism: Porphyromonas gingivalis W83
Primary publication:
Structure determination and analysis of a haemolytic gingipain adhesin domain from Porphyromonas gingivalis.
Li N, Yun P, Nadkarni MA, Ghadikolaee NB, Nguyen KA, Lee M, Hunter N, Collyer CA
Mol Microbiol 76 861-73 (2010)
PMID: 20233299

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157936 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Hemagglutinin A Chains: A, B
Molecule details ›
Chains: A, B
Length: 180 amino acids
Theoretical weight: 19.39 KDa
Source organism: Porphyromonas gingivalis W83
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P59915 (Residues: 1137-1314; Coverage: 8%)
Gene names: PG_1837, hagA
Sequence domains: Cleaved Adhesin Domain
Structure domains: Jelly Rolls

Ligands and Environments

4 bound ligands:
Ligand CA 4 x CA
Ligand SO4 1 x SO4
Ligand NO3 2 x NO3
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1, APS BEAMLINE 23-ID-B
Spacegroup: P21
Unit cell:
a: 29.911Å b: 59.858Å c: 85.672Å
α: 90° β: 94.23° γ: 90°
R-values:
R R work R free
0.177 0.175 0.208
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Dichotomy of gingipains action as virulence factors: from cleaving substrates with the precision of a surgeon's knife to a meat chopper-like brutal degradation of proteins.
Guo et al. (2010)
3 more

3 mentions without citation

Gingipains from Porphyromonas gingivalis - Complex domain structures confer diverse functions.
Li et al. (2011)
2 more