Research workbench
Cryo-EM structure of 5HT3A receptor in presence of alosetron
Analyse Cryo-EM structure of 5HT3A receptor in presence of alosetron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W1J
- Type
- protein
- Length
- 1,965 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- Q8K1F4
- Ligands
- S7Y, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5-hydroxytryptamine receptor 3A | protein | 393 | 39% helix, 25% strand | Q8K1F4 |
Ligands and binding sites
- S7Y · alosetron · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
- CL · Chloride ion · ion
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 | 464 | 0.84 | 0.91 | 67 | empty |
| 2 | 748 | 0.78 | 0.81 | 54 | empty |
| 3 | 154 | 0.77 | 0.93 | 29 | empty |
| 4 | 183 | 0.76 | 0.92 | 20 | S7Y |
| 5 | 184 | 0.76 | 0.92 | 20 | S7Y |
Interfaces
5 interfaces between chains.
- D–E · 3174 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 3142 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 3140 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 3124 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 3074 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6W1J · Cryo-EM structure of 5HT3A receptor in presence of Alosetron · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8K1F4
- Elsewhere: RCSB PDB 6W1J · PDBe 6W1J · UniProt Q8K1F4
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