› 4wsk

X-ray diffraction
1.92Å resolution

Crystal structure of a bacterial fucosidase with phenyl((1R,2R,3R,4R,5R,6R)-2,3,4-trihydroxy-5-methyl-7-azabicyclo[4.1.0]heptan-7-yl)methanone

Released:
DOI: 10.2210/pdb4wsk/pdb
PDB entry 4wsk coloured by chain, front view.
PDB entry 4wsk coloured by chain, side view.
PDB entry 4wsk coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Primary publication:
In vitro and in vivo comparative and competitive activity-based protein profiling of GH29 α-l-fucosidases.
Jiang J, Kallemeijn WW, Wright DW, van den Nieuwendijk AMCH, Rohde VC, Folch EC, van den Elst H, Florea BI, Scheij S, Donker-Koopman WE, Verhoek M, Li N, Schürmann M, Mink D, Boot RG, Codée JDC, van der Marel GA, Davies GJ, Aerts JMFG, Overkleeft HS
Chem Sci 6 2782-false (2015)
PMID: 29142681

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183665 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-L-fucosidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 469 amino acids
Theoretical weight: 54.13 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8A3I4 (Residues: 35-480; Coverage: 98%)
Gene name: BT_2970
Sequence domains: Alpha-L-fucosidase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SO4 6 x SO4
Ligand 3U2 3 x 3U2
Ligand IMD 4 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 55.65Å b: 186.52Å c: 98.15Å
α: 90° β: 94.2° γ: 90°
R-values:
R R work R free
0.185 0.182 0.232
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics.
Kytidou et al. (2020)
3 more

1 mention without citation

In vitro and in vivo comparative and competitive activity-based protein profiling of GH29 α-l-fucosidases.
Jiang et al. (2015)