Research workbench

The crystal structure of IgE Fc mutant - P333C

Analyse The crystal structure of IgE Fc mutant - P333C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LGJ
Type: protein
Length: 624 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: MAN, NAG, BMA, SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	315	9% helix, 49% strand	P01854
B	Ig epsilon chain C region	protein	309	9% helix, 51% strand	P01854

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
PG4 · Tetraethylene glycol · additive · 2 copies · chains A
GOL · Glycerol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	795	0.77	0.81	103	empty
2	58	0.46	0.84	13	empty
3	120	0.39	0.74	20	empty
4	113	0.37	0.74	26	empty
5	110	0.35	0.73	19	empty

Interfaces

1 interface between chains.

A–B · 3084 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5LGJ · The crystal structure of IgE Fc mutant - P333C · the same entry in another collection · chain A against A, TM-score 1.00
P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain A against A, TM-score 0.73

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 P01854
Elsewhere: RCSB PDB 5LGJ · PDBe 5LGJ · UniProt P01854

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.