Research workbench
Crystal structure of CD23 lectin domain mutant D270A
Analyse Crystal structure of CD23 lectin domain mutant D270A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GK1
- Type
- protein
- Length
- 930 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low affinity immunoglobulin epsilon Fc receptor
- UniProt
- P06734
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Low affinity immunoglobulin epsilon Fc receptor | protein | 134 | 15% helix, 34% strand | P06734 |
| B | Low affinity immunoglobulin epsilon Fc receptor | protein | 133 | 15% helix, 40% strand | P06734 |
| C | Low affinity immunoglobulin epsilon Fc receptor | protein | 135 | 15% helix, 37% strand | P06734 |
| D | Low affinity immunoglobulin epsilon Fc receptor | protein | 132 | 15% helix, 34% strand | P06734 |
| F | Low affinity immunoglobulin epsilon Fc receptor | protein | 133 | 15% helix, 33% strand | P06734 |
| G | Low affinity immunoglobulin epsilon Fc receptor | protein | 129 | 18% helix, 36% strand | P06734 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 25 copies · chains A, B, D, C, E, F, G
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.75 | 0.80 | 75 | GOL, SO4 |
| 2 | 806 | 0.72 | 0.78 | 76 | SO4 |
| 3 | 498 | 0.72 | 0.82 | 61 | SO4 |
| 4 | 116 | 0.60 | 0.86 | 24 | SO4 |
| 5 | 282 | 0.53 | 0.75 | 26 | empty |
Interfaces
10 interfaces between chains.
- D–F · 701 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 699 Ų buried · 8 hydrogen bonds · protein-protein
- C–E · 672 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 614 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 378 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 4GK1 · Crystal structure of CD23 lectin domain mutant D270A · the same entry in another collection · chain F against F, 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 G 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 4GK1 · PDBe 4GK1 · UniProt P06734
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