GOLGI MANNOSIDASE II complex with (3R,4R,5R)-3,4-Dihydroxy-5-({[(1R)-2-hydroxy-1 phenylethyl]amino}methyl) methylpyrrolidin-2-one

Structure

x-ray diffraction · resolution 1.74 · 1 distinct chain · 24% helix, 30% strand (DSSP).

Ligands and binding sites

• GB7 · (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-1-methylpyrrolidin-2-one · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• ZN · Zinc ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A
• MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 3DDG · Golgi mannosidase II complex with (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)- 2-hydroxy-1… · 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 3DDG · PDBe 3DDG · UniProt Q24451