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Crystal structure of serum-derived human IGG4 Fc

Analyse Crystal structure of serum-derived human IGG4 Fc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C55
Type: protein
Length: 414 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig gamma-4 chain C region
UniProt: P01861
Ligands: NAG, MAN, BMA, GAL, FUC
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig gamma-4 chain C region	protein	208	11% helix, 49% strand	P01861
B	Ig gamma-4 chain C region	protein	206	11% helix, 49% strand	P01861

Ligands and binding sites

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
GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	80	0.37	0.76	21	empty
2	55	0.29	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 1066 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4C55 · Crystal structure of serum-derived human IgG4 Fc · the same entry in another collection · chain A against A, TM-score 1.00
P01861 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant gamma 4 (P01861) · 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 P01861
Elsewhere: RCSB PDB 4C55 · PDBe 4C55 · UniProt P01861

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