› 6tcv

X-ray diffraction
1.31Å resolution

Crystal structure of Bacteroides thetaiotamicron EndoBT-3987 in complex with Man9GlcNAc2Asn substrate

Released:
DOI: 10.2210/pdb6tcv/pdb
PDB entry 6tcv coloured by chain, front view.
PDB entry 6tcv coloured by chain, side view.
PDB entry 6tcv coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Primary publication:
Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides.
Trastoy B, Du JJ, Klontz EH, Li C, Cifuente JO, Wang LX, Sundberg EJ, Guerin ME
Nat Commun 11 899 (2020)
PMID: 32060313

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-183596 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
BT-3987-like N-terminal domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 451 amino acids
Theoretical weight: 49.13 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8A0N4 (Residues: 27-476; Coverage: 99%)
Gene name: BT_3987
Sequence domains: BT_3987-like, N-terminal domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand ASN 1 x ASN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: R3
Unit cell:
a: 115.495Å b: 115.495Å c: 97.422Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.16 0.159 0.177
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Carbohydrate-active enzymes (CAZymes) in the gut microbiome.
Wardman et al. (2022)
1 more

2 mentions without citation

Sculpting therapeutic monoclonal antibody N-glycans using endoglycosidases.
Trastoy et al. (2022)
1 more