Glycosylated KNOB/DUMMY-hole Fc fragment

Structure

x-ray diffraction · resolution 1.55 · 2 distinct chains · 11% helix, 47% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
• GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1078 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 6YT7 · Glycosylated KNOB/DUMMY-hole Fc fragment · the same entry in another collection · chain A against A, TM-score 1.00
• P0DOX5 · AlphaFold monomer V2.0 prediction for immunoglobulin gamma-1 heavy chain (P0DOX5) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P01857
• Elsewhere: RCSB PDB 6YT7 · PDBe 6YT7 · UniProt P0DOX5 · UniProt P01857