Crystal structure of the class I human endoplasmic reticulum 1,2- alpha-mannosidase T688A mutant and thio-disaccharide substrate analog complex

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).

Ligands and binding sites

• Z5L · methyl 2-thio-alpha-D-mannopyranoside · ligand · 2 copies · chains A, B
• 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 2 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
• CA · Calcium ion · metal · 2 copies · chains A, B
• SO4 · Sulfate ion · ion · 3 copies · chains A, B
• ACT · Acetate ion · additive · 5 copies · chains A, B
• BU1 · 1,4-butanediol · additive · 4 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 348 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

• 5KK7 · Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase T688A… · the same entry in another collection · chain A against A, TM-score 1.00
• Q9UKM7 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum mannosyl- oligosaccharide… · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q9UKM7
• Elsewhere: RCSB PDB 5KK7 · PDBe 5KK7 · UniProt Q9UKM7