MolNFT v1 · #187514 · protein
Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant
7SHT · High affinity immunoglobulin epsilon receptor subunit alpha: “Structure of a partially disrupted IgE high affinity receptor complex bound to an omalizumab variant”. Electron microscopy, 3 ligands (NAG, MAN, BMA), 20 pockets (best…
- PDB
- 7SHT
- Type
- protein
- Length
- 1,259 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity immunoglobulin epsilon receptor subunit alpha; Immunoglobulin heavy…
- UniProt
- P12319, P01854
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | High affinity immunoglobulin epsilon receptor subunit alpha | protein | 167 | 2% helix, 39% strand | P12319 |
| B | Immunoglobulin heavy constant epsilon | protein | 316 | 6% helix, 42% strand | P01854 |
| D | Immunoglobulin heavy constant epsilon | protein | 312 | 7% helix, 37% strand | P01854 |
| H, J | CLONE_7 variable fragment heavy chain | protein | 120 | 3% helix, 53% strand | — |
| K, L | CLONE_7 variable fragment light chain | protein | 112 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, D, K, H, J
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, D
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.81 | 0.83 | 113 | empty |
| 2 | 793 | 0.81 | 0.84 | 109 | empty |
| 3 | 318 | 0.77 | 0.88 | 51 | empty |
| 4 | 535 | 0.77 | 0.84 | 70 | empty |
| 5 | 201 | 0.76 | 0.91 | 38 | empty |
Interfaces
11 interfaces between chains.
- B–D · 1406 Ų buried · 16 hydrogen bonds · protein-protein
- J–K · 610 Ų buried · 2 hydrogen bonds · protein-protein
- H–L · 601 Ų buried · 5 hydrogen bonds · protein-protein
- B–H · 362 Ų buried · 7 hydrogen bonds · protein-protein
- D–J · 331 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7SHT · Structure of a partially disrupted IgE high affinity receptor complex bound to an… · the same entry in another collection · chain L against L, 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 0.90
- 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 0.62
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 7SHT · PDBe 7SHT · UniProt P12319 · UniProt P01854
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