› 4y06

X-ray diffraction
2.18Å resolution

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197666 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidyl aminopeptidase BII Chains: A, B
Molecule details ›
Chains: A, B
Length: 722 amino acids
Theoretical weight: 78.89 KDa
Source organism: Pseudoxanthomonas mexicana
Expression system: Escherichia coli
UniProt:
  • Canonical: V5YM14 (Residues: 1-722; Coverage: 100%)
Gene name: dapb2
Sequence domains: Peptidase S46

Ligands and Environments

4 bound ligands:
Ligand LEU 2 x LEU
Ligand GLU 2 x GLU
Ligand GOL 14 x GOL
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P43212
Unit cell:
a: 122.42Å b: 122.42Å c: 222.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.176 0.235
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis.
Nemoto et al. (2021)
7 other articles

1 mention without citation

Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Sakamoto et al. (2015)