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Crystal structure of human IgE-Fc epsilon 3-4

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

PDB: 5MOI
Type: protein
Length: 1,145 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: MAN, NAG, BMA, PO4
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	177	12% helix, 45% strand	P01854
B	Ig epsilon chain C region	protein	191	10% helix, 47% strand	P01854
C	Ig epsilon chain C region	protein	208	9% helix, 48% strand	P01854
D	Ig epsilon chain C region	protein	193	10% helix, 48% strand	P01854
E	Ig epsilon chain C region	protein	200	11% helix, 48% strand	P01854
F	Ig epsilon chain C region	protein	176	12% helix, 44% strand	P01854

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B, C, D, E, F
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F
PO4 · Phosphate ion · ion · 6 copies · chains B, C, D, E, F
PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, D
EDO · 1,2-ethanediol · additive · chains C

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

Pockets

11 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	830	0.81	0.84	101	PEG
2	350	0.71	0.83	61	empty
3	187	0.44	0.74	28	empty
4	201	0.44	0.73	23	MAN, PEG
5	105	0.42	0.78	21	empty

Interfaces

10 interfaces between chains.

A–B · 1076 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1053 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 983 Å² buried · 6 hydrogen bonds · protein-protein
C–E · 559 Å² buried · 7 hydrogen bonds · protein-protein
A–E · 469 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5MOI · Crystal structure of human IgE-Fc epsilon 3-4 · the same entry in another collection · chain F against F, 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 0.96

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

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