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Crystal structure of the IgE-FC3-4 domains

Analyse Crystal structure of the IgE-FC3-4 domains in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3H9Z
Type: protein
Length: 836 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: NAG, MAN, BMA, NH4
Pockets: 9 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Ig epsilon chain C region	protein	209	10% helix, 47% strand	P01854

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C, D
MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, C, D
BMA · beta-D-mannopyranose · sugar · 3 copies · chains B, C, D
NH4 · Ammonium ion · ion · chains C

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.63	0.93	16	empty
2	237	0.59	0.79	26	empty
3	213	0.54	0.78	30	empty
4	142	0.40	0.74	28	empty
5	171	0.40	0.72	20	empty

Interfaces

3 interfaces between chains.

A–B · 1364 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1327 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 759 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

3H9Z · Crystal structure of the IgE-Fc3-4 domains · 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 0.93

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 3H9Z · PDBe 3H9Z · UniProt P01854

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