Research workbench
The high-affinity complex between IgE and its receptor Fc epsilon ri
Analyse The high-affinity complex between IgE and its receptor Fc epsilon ri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y7Q
- Type
- protein
- Length
- 735 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity immunoglobulin epsilon receptor subunit alpha; Ig epsilon chain C region
- UniProt
- P12319, P01854
- Ligands
- NAG, BMA, MAN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity immunoglobulin epsilon receptor subunit alpha | protein | 158 | 4% helix, 54% strand | P12319 |
| B | Ig epsilon chain C region | protein | 287 | 6% helix, 47% strand | P01854 |
| D | Ig epsilon chain C region | protein | 290 | 6% helix, 46% strand | P01854 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, D
- BMA · beta-D-mannopyranose · sugar · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.71 | 0.76 | 103 | NAG |
| 2 | 66 | 0.55 | 0.88 | 26 | empty |
| 3 | 101 | 0.48 | 0.81 | 24 | empty |
| 4 | 51 | 0.39 | 0.82 | 19 | empty |
| 5 | 114 | 0.38 | 0.74 | 29 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2048 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 2Y7Q · The high-affinity complex between IgE and its receptor Fc epsilon ri · the same entry in another collection · chain A against A, TM-score 1.00
- P12319 · AlphaFold monomer V2.0 prediction for high affinity immunoglobulin epsilon receptor… · a predicted model of the same protein · chain A against A, TM-score 0.96
- P01854 · AlphaFold monomer V2.0 prediction for immunoglobulin heavy constant epsilon (P01854) · a predicted model of the same protein · chain B against A, TM-score 0.70
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
- Every structure of UniProt P01854
- Elsewhere: RCSB PDB 2Y7Q · PDBe 2Y7Q · UniProt P12319 · UniProt P01854
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