› 5kd8

X-ray diffraction
2.3Å resolution

BT_4244 metallopeptidase in complex with Tn antigen.

Released:
DOI: 10.2210/pdb5kd8/pdb
PDB entry 5kd8 coloured by chain, front view.
PDB entry 5kd8 coloured by chain, side view.
PDB entry 5kd8 coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Primary publication:
Recognition of protein-linked glycans as a determinant of peptidase activity.
Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB
Proc Natl Acad Sci U S A 114 E679-E688 (2017)
PMID: 28096352

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183585 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidase M60 domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 559 amino acids
Theoretical weight: 64.27 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q89ZX7 (Residues: 322-857; Coverage: 64%)
Gene name: BT_4244
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand ZN 1 x ZN
Ligand NI 2 x NI
Ligand NA 2 x NA
Ligand SER 1 x SER
Ligand A2G 1 x A2G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P212121
Unit cell:
a: 87.45Å b: 88.23Å c: 98.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.242
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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Citations

9 review citations

Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier.
Martens et al. (2018)
8 more

7 mentions without citation

Molecular Recognition of GalNAc in Mucin-Type O-Glycosylation.
Sanz-Martinez et al. (2023)
6 more