Research workbench
Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 2
Analyse Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J89
- Type
- protein
- Length
- 840 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity immunoglobulin epsilon receptor alpha- subunit
- UniProt
- P12319
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | High affinity immunoglobulin epsilon receptor alpha- subunit | protein | 168 | 5% helix, 46% strand | P12319 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 50 copies · chains A, B, E, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.68 | 0.76 | 64 | empty |
| 2 | 581 | 0.66 | 0.77 | 51 | empty |
| 3 | 276 | 0.55 | 0.76 | 32 | empty |
| 4 | 183 | 0.51 | 0.77 | 21 | empty |
| 5 | 60 | 0.26 | 0.72 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–E · 512 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 437 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 254 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 232 Ų buried · 0 hydrogen bonds · protein-protein
- B–E · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 1J89 · Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 2 · the same entry in another collection · chain C against C, TM-score 1.00
- P12319 · AlphaFold monomer V2.0 prediction for high affinity immunoglobulin epsilon receptor… · a predicted model of the same protein · chain C 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 P12319
- Elsewhere: RCSB PDB 1J89 · PDBe 1J89 · UniProt P12319
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