Crystal structure of the rabbit IgG Fc fragment

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 46% strand (DSSP).

Ligands and binding sites

• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 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
• AZI · Azide ion · ion · 2 copies · chains A, B
• FMT · Formic acid · additive · 6 copies · chains A, B
• GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1000 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2VUO · Crystal structure of the rabbit IgG Fc fragment · the same entry in another collection · chain A against A, TM-score 1.00
• P01870 · AlphaFold monomer V2.0 prediction for ig gamma chain C region (P01870) · a predicted model of the same protein · chain B 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 P01870
• Elsewhere: RCSB PDB 2VUO · PDBe 2VUO · UniProt P01870