MolNFT v1 · #90970 · protein

Crystal structure of the human IgE-FC(EPSILON)3-4 bound to its B cell receptor DERCD23

4EZM · Ig epsilon chain C region: “Crystal structure of the human IgE-FC(EPSILON)3-4 bound to its B cell receptor DERCD23”. X-ray diffraction, 3 ligands (MAN, NAG, BMA), 15 pockets (best druggability 0.59). MolNFT v1 #90970 on GenesisL1…

PDB: 4EZM
Type: protein
Length: 2,022 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ig epsilon chain C region; Low affinity immunoglobulin epsilon Fc receptor
UniProt: P01854, P06734
Ligands: MAN, NAG, BMA
Pockets: 15 · best druggability 0.59

Structure

x-ray diffraction · 9 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	211	9% helix, 46% strand	P01854
B	Ig epsilon chain C region	protein	208	10% helix, 46% strand	P01854
C	Ig epsilon chain C region	protein	197	11% helix, 46% strand	P01854
D	Ig epsilon chain C region	protein	207	10% helix, 47% strand	P01854
E	Ig epsilon chain C region	protein	191	8% helix, 41% strand	P01854
F	Ig epsilon chain C region	protein	208	10% helix, 46% strand	P01854
G, H, I, J	Low affinity immunoglobulin epsilon Fc receptor	protein	133	15% helix, 37% strand	P06734
K	Low affinity immunoglobulin epsilon Fc receptor	protein	134	15% helix, 37% strand	P06734
L	Low affinity immunoglobulin epsilon Fc receptor	protein	134	15% helix, 37% strand	P06734

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 · 12 copies · chains A, B, 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

15 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	140	0.59	0.84	30	empty
2	202	0.49	0.75	25	empty
3	181	0.44	0.74	21	empty
4	167	0.42	0.74	20	empty
5	162	0.41	0.74	24	MAN

Interfaces

12 interfaces between chains.

C–D · 1340 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1328 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1301 Å² buried · 10 hydrogen bonds · protein-protein
F–L · 963 Å² buried · 19 hydrogen bonds · protein-protein
E–K · 938 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4EZM · Crystal structure of the human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23 · the same entry in another collection · chain L against L, TM-score 1.00

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
Every structure of UniProt P06734
Elsewhere: RCSB PDB 4EZM · PDBe 4EZM · UniProt P01854 · UniProt P06734

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