MolNFT v1 · #127169 · protein

Crystal structure of IgE-Fc epsilon 3-4

5MOJ · Ig epsilon chain C region: “Crystal structure of IgE-Fc epsilon 3-4”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 5 pockets (best druggability 0.57). MolNFT v1 #127169 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MOJ
Type: protein
Length: 400 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: NAG, MAN, BMA, SO4
Pockets: 5 · best druggability 0.57

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	203	10% helix, 48% strand	P01854
B	Ig epsilon chain C region	protein	197	11% helix, 49% strand	P01854

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 7 copies · chains A, B
EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

5 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	81	0.57	0.87	16	empty
2	101	0.55	0.84	19	empty
3	96	0.47	0.81	30	SO4
4	105	0.34	0.73	21	PEG
5	100	0.33	0.73	20	SO4

Interfaces

1 interface between chains.

A–B · 1115 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5MOJ · Crystal structure of IgE-Fc epsilon 3-4 · 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 0.96

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 5MOJ · PDBe 5MOJ · UniProt P01854

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