MolNFT v1 · #92808 · protein
Crystal structure of CD23 lectin domain mutant D258A
4GJX · Low affinity immunoglobulin epsilon Fc receptor: “Crystal structure of CD23 lectin domain mutant D258A”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #92808 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4GJX
- Type
- protein
- Length
- 1,078 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 0.79
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G | Low affinity immunoglobulin epsilon Fc receptor | protein | 135 | 17% helix, 38% strand | P06734 |
| C, H | Low affinity immunoglobulin epsilon Fc receptor | protein | 134 | 17% helix, 38% strand | P06734 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.79 | 0.80 | 108 | GOL |
| 2 | 1009 | 0.78 | 0.80 | 118 | empty |
| 3 | 868 | 0.77 | 0.80 | 89 | empty |
| 4 | 251 | 0.53 | 0.76 | 24 | empty |
| 5 | 63 | 0.48 | 0.85 | 18 | empty |
Interfaces
12 interfaces between chains.
- A–D · 590 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 581 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 580 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 389 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 332 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 4GJX · Crystal structure of CD23 lectin domain mutant D258A · 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 0.96
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 4GJX · PDBe 4GJX · UniProt P06734
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