Research workbench
Mouse serotonin 5HT3 receptor in complex with palonosetron
Analyse Mouse serotonin 5HT3 receptor in complex with palonosetron in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y1Z
- Type
- protein
- Length
- 1,930 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 0.84
Structure
electron microscopy · 1 distinct chain · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, B, C, E | 5-hydroxytryptamine receptor 3A | protein | 386 | 41% helix, 26% 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, B, D, E, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, D, B, C, 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 | 969 | 0.84 | 0.85 | 131 | empty |
| 2 | 595 | 0.83 | 0.87 | 48 | empty |
| 3 | 692 | 0.82 | 0.86 | 60 | empty |
| 4 | 517 | 0.79 | 0.85 | 75 | empty |
| 5 | 483 | 0.78 | 0.85 | 68 | empty |
Interfaces
5 interfaces between chains.
- A–E · 3399 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3373 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3373 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 3341 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 3338 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6Y1Z · Mouse serotonin 5HT3 receptor in complex with 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 6Y1Z · PDBe 6Y1Z · UniProt Q8K1F4
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