Research workbench
Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 1
Analyse Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J88
- 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, MAN
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | High affinity immunoglobulin epsilon receptor alpha- subunit | protein | 168 | 4% helix, 49% strand | P12319 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 43 copies · chains A, B, E, C, D
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.69 | 0.77 | 56 | empty |
| 2 | 579 | 0.67 | 0.77 | 54 | empty |
| 3 | 395 | 0.55 | 0.74 | 33 | empty |
| 4 | 233 | 0.48 | 0.74 | 20 | empty |
| 5 | 95 | 0.39 | 0.76 | 21 | NAG |
Interfaces
6 interfaces between chains.
- B–D · 625 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 591 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 508 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 503 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 97 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 glycan, 10 disulfide (N-glycosylation, disulfide).
Compared structures
- 1J88 · Human high affinity Fc receptor FC(EPSILON)RI(ALPHA), tetragonal crystal form 1 · the same entry in another collection · chain E against E, TM-score 1.00
- P12319 · AlphaFold monomer V2.0 prediction for high affinity immunoglobulin epsilon receptor… · a predicted model of the same protein · chain D 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 1J88 · PDBe 1J88 · UniProt P12319
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