Fc fragment of IGG1 (herceptin) with protein-a mimetic peptide dendrimer ligand.

Structure

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

Ligands and binding sites

• X12 · 2-[[(2S)-2,6-bis[[(2S)-2,6-bis[[(2R)-2-[[(2R,3R)-2-[[(2R)-2-amino-5-carbamimidamido-pentanoyl]amino]-3-hydroxy-butanoyl]amino]-3-(4-hydroxyphenyl)propanoyl]amino]hexanoyl]amino]hexanoyl]amino]ethanoic acid · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
• BMA · beta-D-mannopyranose · 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.

Interfaces

1 interface between chains.

• A–B · 1157 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 3D6G · Fc fragment of IgG1 (Herceptin) with protein-A mimetic peptide dendrimer ligand. · the same entry in another collection · chain A against A, TM-score 1.00
• P01857 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 1 (P01857) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P01857
• Elsewhere: RCSB PDB 3D6G · PDBe 3D6G · UniProt P01857