Research workbench
Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation
Analyse Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HIS
- Type
- protein
- Length
- 1,935 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- P23979
- Ligands
- TKT, NAG, BMA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, B, C, D | 5-hydroxytryptamine receptor 3A | protein | 387 | 41% helix, 27% strand | P23979 |
Ligands and binding sites
- TKT · (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate · ligand · 5 copies · chains A, B, E, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, E, C, D
- BMA · beta-D-mannopyranose · sugar · 5 copies
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 | 1099 | 0.88 | 0.89 | 139 | empty |
| 2 | 688 | 0.79 | 0.83 | 73 | empty |
| 3 | 767 | 0.78 | 0.82 | 87 | empty |
| 4 | 1117 | 0.78 | 0.80 | 121 | empty |
| 5 | 742 | 0.77 | 0.81 | 75 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3323 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 3322 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 3313 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 3300 Ų buried · 19 hydrogen bonds · protein-protein
- E–D · 3290 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HIS · Mouse serotonin 5-HT3 receptor, tropisetron-bound, T conformation · the same entry in another collection · chain D against D, TM-score 1.00
- P23979 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 3A (P23979) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P23979
- Elsewhere: RCSB PDB 6HIS · PDBe 6HIS · UniProt P23979
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