Golgi mannosidase II D204A catalytic nucleophile mutant complex with methyl (2-deoxy-2-acetamido-beta-D-glucopyranosyl)-(1->2)-alpha-D- mannopyranosyl- (1->3)-[alpha-D-mannopyranosyl-(1->6)-6-thio-alpha-D- mannopyranosyl- (1->6)]-beta-D-mannopyranoside

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 31% strand (DSSP).

Ligands and binding sites

• YZ0 · methyl beta-D-mannopyranoside · ligand · chains A
• Z4Y · 6-thio-alpha-D-mannopyranose · ligand · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• ZN · Zinc ion · metal · chains A
• MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

• 3BVW · GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl… · the same entry in another collection · chain A against A, TM-score 1.00
• Q24451 · AlphaFold monomer V2.0 prediction for alpha-mannosidase 2 (Q24451) · 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 Q24451
• Elsewhere: RCSB PDB 3BVW · PDBe 3BVW · UniProt Q24451