Research workbench
Cryo-EM structure of 5HT3A receptor in presence of granisetron
Analyse Cryo-EM structure of 5HT3A receptor in presence of granisetron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NP0
- Type
- protein
- Length
- 1,975 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.92
- Source
- Mus musculus
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- E9QLC0
- Ligands
- CWB, NAG, BMA, CL
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 2.92 · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5-hydroxytryptamine receptor 3A | protein | 395 | 37% helix, 26% strand | E9QLC0 |
Ligands and binding sites
- CWB · 1-methyl-N-[(1R,5S)-9-methyl-9-azabicyclo[3.3.1]nonan-3-yl]indazole-3-carboxamide · 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 | 718 | 0.87 | 0.90 | 97 | empty |
| 2 | 330 | 0.80 | 0.89 | 41 | empty |
| 3 | 241 | 0.77 | 0.90 | 37 | empty |
| 4 | 216 | 0.76 | 0.90 | 35 | empty |
| 5 | 780 | 0.75 | 0.79 | 51 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3152 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3062 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 3006 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2921 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 2911 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 6NP0 · Cryo-EM structure of 5HT3A receptor in presence of granisetron · 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 E9QLC0
- Elsewhere: RCSB PDB 6NP0 · PDBe 6NP0 · UniProt E9QLC0
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