MolNFT v1 · #92480 · protein
Crystal structure of CALCIUM2+-bound wild-type CD23 lectin domain
4G9A · Low affinity immunoglobulin epsilon Fc receptor: “Crystal structure of CALCIUM2+-bound wild-type CD23 lectin domain”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.76). MolNFT v1 #92480 on GenesisL1: 3D structure…
- PDB
- 4G9A
- Type
- protein
- Length
- 526 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
- CA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 15% helix, 35% strand | P06734 |
| B | Low affinity immunoglobulin epsilon Fc receptor | protein | 135 | 14% helix, 35% strand | P06734 |
| C | Low affinity immunoglobulin epsilon Fc receptor | protein | 130 | 15% helix, 36% strand | P06734 |
| D | Low affinity immunoglobulin epsilon Fc receptor | protein | 129 | 15% helix, 36% strand | P06734 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 3 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1121 | 0.76 | 0.78 | 105 | GOL |
| 2 | 238 | 0.53 | 0.77 | 28 | empty |
| 3 | 62 | 0.50 | 0.86 | 18 | CA |
| 4 | 78 | 0.42 | 0.79 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–C · 772 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 629 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 491 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 212 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 140 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4G9A · Crystal structure of calcium2+-bound wild-type CD23 lectin domain · 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 C 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 4G9A · PDBe 4G9A · UniProt P06734
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