Research workbench
Cryo-EM structure of 5HT3A receptor in presence of palonosetron
Analyse Cryo-EM structure of 5HT3A receptor in presence of palonosetron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W1Y
- Type
- protein
- Length
- 1,970 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- Q8K1F4
- Ligands
- O7B, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5-hydroxytryptamine receptor 3A | protein | 394 | 36% helix, 24% strand | Q8K1F4 |
Ligands and binding sites
- O7B · (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one · 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
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 | 642 | 0.86 | 0.90 | 85 | empty |
| 2 | 914 | 0.79 | 0.81 | 54 | empty |
| 3 | 227 | 0.77 | 0.90 | 40 | empty |
| 4 | 202 | 0.75 | 0.90 | 36 | empty |
| 5 | 164 | 0.73 | 0.90 | 28 | empty |
Interfaces
5 interfaces between chains.
- D–E · 3045 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 3035 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 3017 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2998 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 2978 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6W1Y · Cryo-EM structure of 5HT3A receptor in presence of Palonosetron · 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 6W1Y · PDBe 6W1Y · UniProt Q8K1F4
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