MolNFT v1 · #127170 · protein

Crystal structure of human IgE-Fc epsilon 3-4

5MOK · Ig epsilon chain C region: “Crystal structure of human IgE-Fc epsilon 3-4”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 7 pockets (best druggability 0.62). MolNFT v1 #127170 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5MOK
Type: protein
Length: 813 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: MAN, NAG, BMA
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	208	10% helix, 48% strand	P01854
B	Ig epsilon chain C region	protein	205	10% helix, 48% strand	P01854
C	Ig epsilon chain C region	protein	198	10% helix, 48% strand	P01854
D	Ig epsilon chain C region	protein	202	10% helix, 48% strand	P01854

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D

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

Pockets

7 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	58	0.62	0.92	16	empty
2	131	0.44	0.77	21	empty
3	156	0.44	0.75	25	empty
4	186	0.43	0.73	24	MAN
5	128	0.37	0.73	20	empty

Interfaces

3 interfaces between chains.

A–B · 1205 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 1148 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 627 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

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

Compared structures

5MOK · Crystal structure of human IgE-Fc epsilon 3-4 · the same entry in another collection · chain D against D, TM-score 1.00
P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 5MOK · PDBe 5MOK · UniProt P01854

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