› 3wom

X-ray diffraction
1.86Å resolution

Crystal structure of the DAP BII dipeptide complex II

Released:
DOI: 10.2210/pdb3wom/pdb
PDB entry 3wom coloured by chain, front view.
PDB entry 3wom coloured by chain, side view.
PDB entry 3wom 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: 76.39 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

4 bound ligands:
Ligand VAL 2 x VAL
Ligand TYR 2 x TYR
Ligand GOL 10 x GOL
Ligand ZN 4 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: 122.22Å b: 122.22Å c: 219.76Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 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

1 mention without citation

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