Research workbench
Crystal structure of CD23 lectin domain mutant S252A
Analyse Crystal structure of CD23 lectin domain mutant S252A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GJ0
- Type
- protein
- Length
- 531 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low affinity immunoglobulin epsilon Fc receptor
- UniProt
- P06734
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity immunoglobulin epsilon Fc receptor | protein | 135 | 14% helix, 36% strand | P06734 |
| B | Low affinity immunoglobulin epsilon Fc receptor | protein | 134 | 14% helix, 36% strand | P06734 |
| C | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 14% helix, 37% strand | P06734 |
| D | Low affinity immunoglobulin epsilon Fc receptor | protein | 130 | 15% helix, 35% strand | P06734 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.79 | 0.81 | 81 | SO4, GOL |
| 2 | 141 | 0.44 | 0.76 | 27 | empty |
| 3 | 102 | 0.39 | 0.76 | 24 | empty |
| 4 | 61 | 0.27 | 0.73 | 18 | GOL |
Interfaces
5 interfaces between chains.
- A–C · 676 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 670 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 524 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 420 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 417 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 4GJ0 · Crystal structure of CD23 lectin domain mutant S252A · the same entry in another collection · chain D against D, 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 D 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 4GJ0 · PDBe 4GJ0 · UniProt P06734
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