Crystal structure of glycosylated myelin-associated glycoprotein (mag) IG1-3 with soaked trisaccharide ligand

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
• GAL · beta-D-galactopyranose · sugar · chains B
• SIA · N-acetyl-alpha-neuraminic acid · sugar · chains B
• SO4 · Sulfate ion · ion · 9 copies · chains A, B
• GOL · Glycerol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1555 Ų buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 glycan, 8 disulfide (disulfide, N-glycosylation, C-mannosylation).

Compared structures

• 5LFV · Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked… · the same entry in another collection · chain A against A, TM-score 1.00
• P20917 · AlphaFold monomer V2.0 prediction for myelin-associated glycoprotein (P20917) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P20917
• Elsewhere: RCSB PDB 5LFV · PDBe 5LFV · UniProt P20917