Research workbench
High affinity IgE receptor (alpha chain) complexed with tight-binding E131 'zeta' peptide from phage display
Analyse High affinity IgE receptor (alpha chain) complexed with tight-binding E131… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RPQ
- Type
- protein
- Length
- 746 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity immunoglobulin epsilon receptor alpha-subunit precursor; Peptide E131
- UniProt
- P12319
- Ligands
- NAG, BMA, SO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity immunoglobulin epsilon receptor alpha-subunit precursor | protein | 165 | 5% helix, 53% strand | P12319 |
| B | High affinity immunoglobulin epsilon receptor alpha-subunit precursor | protein | 164 | 5% helix, 53% strand | P12319 |
| C | High affinity immunoglobulin epsilon receptor alpha-subunit precursor | protein | 166 | 5% helix, 53% strand | P12319 |
| D | High affinity immunoglobulin epsilon receptor alpha-subunit precursor | protein | 167 | 5% helix, 52% strand | P12319 |
| W, X, Y, Z | Peptide E131 | protein | 21 | 33% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, Y, B, Z, C, D, X
- BMA · beta-D-mannopyranose · sugar · 16 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, Y, B, Z
- CIT · Citric acid · additive · 2 copies · chains A, C, B, D
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 | 729 | 0.70 | 0.77 | 81 | CIT |
| 2 | 613 | 0.66 | 0.76 | 60 | empty |
| 3 | 195 | 0.52 | 0.77 | 29 | SO4 |
| 4 | 148 | 0.51 | 0.79 | 23 | CIT |
| 5 | 169 | 0.51 | 0.78 | 26 | SO4 |
Interfaces
15 interfaces between chains.
- D–Z · 458 Ų buried · 6 hydrogen bonds · protein-protein
- B–X · 452 Ų buried · 5 hydrogen bonds · protein-protein
- C–Y · 447 Ų buried · 5 hydrogen bonds · protein-protein
- A–W · 441 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 415 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 1RPQ · High Affinity IgE Receptor (alpha chain) Complexed with Tight-Binding E131 'zeta' Peptide… · the same entry in another collection · chain Z against Z, 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 0.98
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 P12319
- Elsewhere: RCSB PDB 1RPQ · PDBe 1RPQ · UniProt P12319
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