Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated soluble form of Fc gamma receptor iiia

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, B
• MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
• GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
• CL · Chloride ion · ion · 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, 0 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1172 Ų buried · 8 hydrogen bonds · protein-protein
• A–C · 579 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 401 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 5XJF · Crystal structure of fucosylated IgG Fc Y296W mutant complexed with bis-glycosylated… · the same entry in another collection · chain A against A, TM-score 1.00
• P08637 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin gamma Fc region… · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P0DOX5
• Every structure of UniProt P08637
• Elsewhere: RCSB PDB 5XJF · PDBe 5XJF · UniProt P0DOX5 · UniProt P08637