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Crystal structure of IgG Fc with a homogeneous glycoform and antibody- dependent cellular cytotoxicity

Analyse Crystal structure of IgG Fc with a homogeneous glycoform and antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GSQ
Type: protein
Length: 818 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig gamma-1 chain C region
UniProt: P01857
Ligands: NAG, MAN, BMA, GAL, SIA
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Ig gamma-1 chain C region	protein	208	11% helix, 49% strand	P01857
D	Ig gamma-1 chain C region	protein	194	11% helix, 46% strand	P01857

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
SIA · N-acetyl-alpha-neuraminic acid · sugar

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	316	0.62	0.80	35	empty
2	376	0.60	0.77	34	empty
3	145	0.42	0.74	31	empty
4	130	0.40	0.75	30	empty
5	79	0.33	0.75	19	empty

Interfaces

4 interfaces between chains.

A–B · 1132 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 1104 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 210 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 72 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

5GSQ · Crystal structure of IgG Fc with a homogeneous glycoform and Antibody-Dependent Cellular… · the same entry in another collection · chain A against A, TM-score 1.00

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 5GSQ · PDBe 5GSQ · UniProt P01857

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