› 5ne5

X-ray diffraction
1.05Å resolution

Crystal structure of family 47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with kifunensine

Released:
DOI: 10.2210/pdb5ne5/pdb
PDB 5ne5 coloured by chain and viewed from the front.
PDB 5ne5 coloured by chain and viewed from the side.
PDB 5ne5 coloured by chain and viewed from the top.
Source organism: Caulobacter sp. K31
Primary publication:
Conformational analysis of the mannosidase inhibitor kifunensine: a quantum mechanical and structural approach.
Males A, Raich L, Williams SJ, Rovira C, Davies GJ
Chembiochem (2017)
PMID: 28493500

Function and Biology Details

Reaction catalysed: 
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mannosyl-oligosaccharide 1,2-alpha-mannosidase Chain: A
Molecule details ›
Chain: A
Length: 447 amino acids
Theoretical weight: 50.55 KDa
Source organism: Caulobacter sp. K31
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0SWV2 (Residues: 27-462; Coverage: 100%)
Gene name: Caul_4035
Sequence domains: Glycosyl hydrolase family 47
Structure domains: Glycosyltransferase

Ligands and Environments

4 bound ligands:
Ligand KIF 1 x KIF
Ligand CA 2 x CA
Ligand BTB 1 x BTB
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: R3
Unit cell:
a: 144.923Å b: 144.923Å c: 50.593Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.146 0.146 0.152
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Natural products as modulators of eukaryotic protein secretion.
Luesch et al. (2020)
3 other articles