MolNFT v1 · #95987 · protein

Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain (crystal form C)

4J6L · Low affinity immunoglobulin epsilon Fc receptor: “Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain (crystal form C)”. X-ray diffraction, 8 pockets (best druggability 0.80). MolNFT v1 #95987 on GenesisL1: 3D…

PDB: 4J6L
Type: protein
Length: 1,053 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Low affinity immunoglobulin epsilon Fc receptor
UniProt: P06734
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 8 distinct chains · 14% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Low affinity immunoglobulin epsilon Fc receptor	protein	133	14% helix, 38% strand	P06734
B	Low affinity immunoglobulin epsilon Fc receptor	protein	133	14% helix, 38% strand	P06734
C	Low affinity immunoglobulin epsilon Fc receptor	protein	132	14% helix, 41% strand	P06734
D	Low affinity immunoglobulin epsilon Fc receptor	protein	133	14% helix, 38% strand	P06734
E	Low affinity immunoglobulin epsilon Fc receptor	protein	130	15% helix, 38% strand	P06734
F	Low affinity immunoglobulin epsilon Fc receptor	protein	128	15% helix, 35% strand	P06734
G	Low affinity immunoglobulin epsilon Fc receptor	protein	135	14% helix, 38% strand	P06734
H	Low affinity immunoglobulin epsilon Fc receptor	protein	129	15% helix, 36% strand	P06734

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.80	0.95	43	empty
2	888	0.80	0.82	68	empty
3	605	0.66	0.76	56	empty
4	264	0.54	0.76	27	empty
5	253	0.51	0.75	35	empty

Interfaces

13 interfaces between chains.

A–G · 706 Å² buried · 13 hydrogen bonds · protein-protein
C–H · 698 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 672 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 643 Å² buried · 8 hydrogen bonds · protein-protein
C–G · 443 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4J6L · Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form C) · the same entry in another collection · chain H against H, TM-score 1.00
P06734 · AlphaFold monomer V2.0 prediction for low affinity immunoglobulin epsilon Fc receptor… · a predicted model of the same protein · chain C against A, TM-score 0.99

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 P06734
Elsewhere: RCSB PDB 4J6L · PDBe 4J6L · UniProt P06734

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