MolNFT v1 · #95988 · protein

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

4J6M · Low affinity immunoglobulin epsilon Fc receptor: “Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain (crystal form D)”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability 0.83). MolNFT v1 #95988 on…

PDB: 4J6M
Type: protein
Length: 1,062 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Low affinity immunoglobulin epsilon Fc receptor
UniProt: P06734
Ligands: SO4
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 14% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Low affinity immunoglobulin epsilon Fc receptor	protein	135	14% helix, 38% strand	P06734
D, E	Low affinity immunoglobulin epsilon Fc receptor	protein	134	14% helix, 34% strand	P06734
F	Low affinity immunoglobulin epsilon Fc receptor	protein	131	15% helix, 39% strand	P06734
G, H	Low affinity immunoglobulin epsilon Fc receptor	protein	129	15% helix, 36% strand	P06734

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, E, G, B, H, C, D, F

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

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	963	0.83	0.84	93	empty
2	163	0.76	0.93	43	SO4
3	595	0.67	0.77	71	empty
4	351	0.57	0.76	36	empty
5	302	0.54	0.75	29	empty

Interfaces

14 interfaces between chains.

A–G · 721 Å² buried · 16 hydrogen bonds · protein-protein
B–H · 707 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 694 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 668 Å² buried · 17 hydrogen bonds · protein-protein
C–H · 495 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

4J6M · Crystal structure of calcium2+-free wild-type CD23 lectin domain (crystal form D) · 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 F against A, TM-score 0.98

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 4J6M · PDBe 4J6M · UniProt P06734

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