We've built a new version of this page with an interactive 3D viewer. Try it out in beta and help us improve:

› 6lgd

X-ray diffraction
1.75Å resolution

Bombyx mori GH13 sucrose hydrolase complexed with 1,4-dideoxy-1,4-imino-D-arabinitol

Released:
DOI: 10.2210/pdb6lgd/pdb
Model geometry
Fit model/data
PDB entry 6lgd coloured by chain, front view.
PDB entry 6lgd coloured by chain, side view.
PDB entry 6lgd coloured by chain, top view.
Source organism: Bombyx mori
Primary publication:
Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17 exo-α-glucosidases.
Miyazaki T, Park EY
J Biol Chem 295 8784-8797 (2020)
PMID: 32381508

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucoseresidues with release of alpha-D-glucose.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100531 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
alpha-glucosidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 598 amino acids
Theoretical weight: 68.74 KDa
Source organism: Bombyx mori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A077JI83 (Residues: 30-606; Coverage: 95%)
Gene names: 101745623, BmSuh
Sequence domains: Alpha amylase, catalytic domain

Ligands and Environments

5 bound ligands:
Ligand MG 4 x MG
Ligand CA 2 x CA
Ligand 1AB 2 x 1AB
Ligand GOL 5 x GOL
Ligand PGE 1 x PGE
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P212121
Unit cell:
a: 65.054Å b: 146.444Å c: 153.291Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.162 0.184
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 citation in other articles

Stereoselective synthesis of a 4-⍺-glucoside of valienamine and its X-ray structure in complex with Streptomyces coelicolor GlgE1-V279S.
Si et al. (2021)
3 more

2 mentions without citation

The chemistry and biology of natural ribomimetics and related compounds.
Tsunoda et al. (2022)
1 more