MolNFT v1 · #65881 · protein

Crystal structure of the IgE-FC3-4 domains

3HA0 · Ig epsilon chain C region: “Crystal structure of the IgE-FC3-4 domains”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 14 pockets (best druggability 0.70). MolNFT v1 #65881 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3HA0
Type: protein
Length: 1,254 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region
UniProt: P01854
Ligands: NAG, MAN, BMA
Pockets: 14 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	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 · 12 copies · chains A, B, C, D, E, F
MAN · alpha-D-mannopyranose · sugar · 12 copies · chains A, C, D, E, F
BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B, C, D, E, F

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

Pockets

14 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	677	0.70	0.77	88	empty
2	141	0.55	0.82	22	empty
3	266	0.55	0.77	43	empty
4	63	0.46	0.83	16	empty
5	91	0.44	0.80	19	empty

Interfaces

10 interfaces between chains.

A–B · 1372 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1307 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 1138 Å² buried · 13 hydrogen bonds · protein-protein
C–F · 649 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 602 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

3HA0 · Crystal structure of the IgE-Fc3-4 domains · the same entry in another collection · chain E against E, 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 0.90

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 3HA0 · PDBe 3HA0 · UniProt P01854

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