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Crystal structure of the CALCIUM2+-bound human IgE-FC(EPSILON)3-4 bound to its B cell receptor DERCD23

Analyse Crystal structure of the CALCIUM2+-bound human IgE-FC(EPSILON)3-4 bound to its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4GKO
Type: protein
Length: 1,987 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, CA
Pockets: 16 · best druggability 0.70

Structure

x-ray diffraction · 11 distinct chains · 12% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ig epsilon chain C region	protein	209	9% helix, 44% strand	P01854
B	Ig epsilon chain C region	protein	207	10% helix, 45% strand	P01854
C	Ig epsilon chain C region	protein	197	11% helix, 47% strand	P01854
D	Ig epsilon chain C region	protein	189	11% helix, 35% strand	P01854
E	Ig epsilon chain C region	protein	180	8% helix, 37% strand	P01854
F	Ig epsilon chain C region	protein	197	11% helix, 44% strand	P01854
G, J	Low affinity immunoglobulin epsilon Fc receptor	protein	135	15% helix, 36% strand	P06734
H	Low affinity immunoglobulin epsilon Fc receptor	protein	133	15% helix, 35% strand	P06734
I	Low affinity immunoglobulin epsilon Fc receptor	protein	134	15% helix, 36% strand	P06734
K	Low affinity immunoglobulin epsilon Fc receptor	protein	135	15% helix, 36% strand	P06734
L	Low affinity immunoglobulin epsilon Fc receptor	protein	136	15% helix, 35% 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
CA · Calcium ion · metal · 6 copies · chains G, H, I, J, K, L

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

Pockets

16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	499	0.70	0.80	59	empty
2	64	0.62	0.92	24	empty
3	74	0.62	0.91	27	empty
4	85	0.59	0.87	19	empty
5	90	0.57	0.86	20	empty

Interfaces

13 interfaces between chains.

C–D · 1315 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1312 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1088 Å² buried · 11 hydrogen bonds · protein-protein
B–H · 904 Å² buried · 18 hydrogen bonds · protein-protein
A–G · 887 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

4GKO · Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell… · the same entry in another collection · chain K against K, 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 4GKO · PDBe 4GKO · UniProt P01854 · UniProt P06734

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