› 3wok

X-ray diffraction
1.95Å resolution

Crystal structure of the DAP BII (Space)

Released:
DOI: 10.2210/pdb3wok/pdb
PDB entry 3wok coloured by chain, front view.
PDB entry 3wok coloured by chain, side view.
PDB entry 3wok coloured by chain, top view.
Source organism: Pseudoxanthomonas mexicana
Primary publication:
S46 peptidases are the first exopeptidases to be members of clan PA.
Sakamoto Y, Suzuki Y, Iizuka I, Tateoka C, Roppongi S, Fujimoto M, Inaka K, Tanaka H, Masaki M, Ohta K, Okada H, Nonaka T, Morikawa Y, Nakamura KT, Ogasawara W, Tanaka N
Sci Rep 4 4977 (2014)
PMID: 24827749

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-197667 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dipeptidyl aminopeptidase BII Chains: A, B
Molecule details ›
Chains: A, B
Length: 698 amino acids
Theoretical weight: 77.08 KDa
Source organism: Pseudoxanthomonas mexicana
Expression system: Escherichia coli
UniProt:
  • Canonical: V5YM14 (Residues: 25-722; Coverage: 100%)
Gene name: dapb2
Sequence domains: Peptidase S46

Ligands and Environments

2 bound ligands:
Ligand GOL 11 x GOL
Ligand ZN 4 x ZN
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 76.74Å b: 130.44Å c: 171.46Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.182 0.225
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Exopeptidases and gingipains in Porphyromonas gingivalis as prerequisites for its amino acid metabolism.
Nemoto et al. (2016)
2 more

2 mentions without citation

S46 peptidases are the first exopeptidases to be members of clan PA.
Sakamoto et al. (2014)
1 more