MolNFT v1 · #127171 · protein

Human IgE-Fc crystal structure

5MOL · Ig epsilon chain C region: “Human IgE-Fc crystal structure”. X-ray diffraction, 4 ligands (AE3, MAN, NAG), 12 pockets (best druggability 0.67). MolNFT v1 #127171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5MOL
Type: protein
Length: 640 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: AE3, MAN, NAG, BMA
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	318	10% helix, 48% strand	P01854
B	Ig epsilon chain C region	protein	322	9% helix, 49% strand	P01854

Ligands and binding sites

AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · chains B
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
EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

12 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	253	0.67	0.84	39	empty
2	50	0.54	0.90	16	empty
3	51	0.53	0.89	22	empty
4	122	0.49	0.80	25	empty
5	208	0.47	0.75	32	empty

Interfaces

1 interface between chains.

A–B · 2927 Å² buried · 38 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5MOL · Human IgE-Fc crystal structure · 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 5MOL · PDBe 5MOL · UniProt P01854

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