› 5wdl

X-ray diffraction
2.62Å resolution

A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis

Released:
DOI: 10.2210/pdb5wdl/pdb
PDB 5wdl coloured by chain and viewed from the front.
PDB 5wdl coloured by chain and viewed from the side.
PDB 5wdl coloured by chain and viewed from the top.
Source organism: Parabacteroides distasonis ATCC 8503
Primary publication:
A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Xu JH, Jiang Z, Solania A, Chatterjee S, Suzuki B, Lietz CB, Hook VYH, O'Donoghue AJ, Wolan DW
ACS Chem. Biol. 13 2513-2521 (2018)
PMID: 30085657

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Aminopeptidase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 401 amino acids
Theoretical weight: 45.9 KDa
Source organism: Parabacteroides distasonis ATCC 8503
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: A6LE66 (Residues: 23-405; Coverage: 100%)
Gene name: BDI_2249
Sequence domains: Peptidase C1-like family
Structure domains: Cysteine proteinases

Ligands and Environments

2 bound ligands:
Ligand R33 6 x R33
Ligand K 12 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P212121
Unit cell:
a: 104.841Å b: 140.299Å c: 221.087Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.171 0.212
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

1 review citation

Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health.
Ezeji et al. (2021)
1 other article