Research workbench
Full-length 5-HT3A receptor in a serotonin-bound conformation- state 2
Analyse Full-length 5-HT3A receptor in a serotonin-bound conformation- state 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DG8
- Type
- protein
- Length
- 1,955 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- E9QLC0
- Ligands
- SRO, NAG, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5-hydroxytryptamine receptor 3A | protein | 391 | 39% helix, 23% strand | E9QLC0 |
Ligands and binding sites
- SRO · Serotonin · 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 | 658 | 0.87 | 0.91 | 81 | empty |
| 2 | 619 | 0.86 | 0.90 | 86 | empty |
| 3 | 403 | 0.86 | 0.93 | 48 | empty |
| 4 | 527 | 0.85 | 0.91 | 69 | empty |
| 5 | 250 | 0.83 | 0.94 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–E · 2660 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2650 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 2613 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2578 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 2466 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6DG8 · Full-length 5-HT3A receptor in a serotonin-bound conformation- State 2 · 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 6DG8 · PDBe 6DG8 · UniProt E9QLC0
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