Research workbench
Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain
Analyse Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G96
- Type
- protein
- Length
- 533 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
- 3 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Low affinity immunoglobulin epsilon Fc receptor | protein | 135 | 15% helix, 37% strand | P06734 |
| C | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 14% helix, 37% strand | P06734 |
| D | Low affinity immunoglobulin epsilon Fc receptor | protein | 131 | 15% helix, 35% strand | P06734 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.80 | 0.81 | 95 | empty |
| 2 | 85 | 0.36 | 0.76 | 20 | empty |
| 3 | 75 | 0.32 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- B–D · 704 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 642 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 448 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 399 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4G96 · Crystal structure of calcium2+-free 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 4G96 · PDBe 4G96 · UniProt P06734
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