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Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain (crystal form D)
Analyse Crystal structure of CALCIUM2+-free wild-type CD23 lectin domain (crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 16 hydrogen bonds · protein-protein
- B–H · 707 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 694 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 668 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 495 Ų 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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