Research workbench
Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation
Analyse Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HIO
- Type
- protein
- Length
- 1,925 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Mus musculus
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- P23979
- Ligands
- SRO, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 4.2 · 1 distinct chain · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, B, C, D | 5-hydroxytryptamine receptor 3A | protein | 385 | 41% helix, 24% strand | P23979 |
Ligands and binding sites
- SRO · Serotonin · ligand · 5 copies · chains A, B, E, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, E, B, C, D
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 | 990 | 0.84 | 0.85 | 97 | empty |
| 2 | 1117 | 0.82 | 0.82 | 111 | empty |
| 3 | 1083 | 0.81 | 0.82 | 105 | empty |
| 4 | 549 | 0.80 | 0.86 | 64 | empty |
| 5 | 733 | 0.79 | 0.83 | 77 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3354 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3214 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 3176 Ų buried · 16 hydrogen bonds · protein-protein
- E–D · 3173 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 3127 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 6HIO · Mouse serotonin 5-HT3 receptor, serotonin-bound, I1 conformation · the same entry in another collection · chain E against E, TM-score 1.00
- P23979 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 3A (P23979) · a predicted model of the same protein · chain E 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 6HIO · PDBe 6HIO · UniProt P23979
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