MolNFT v1 · #143927 · protein
Cryo-EM structure of serotonin receptor
6BE1 · 5-hydroxytryptamine receptor 3A: “Cryo-EM structure of serotonin receptor”. Electron microscopy, 5 ligands (PX4, NAG, BMA), 20 pockets (best druggability 0.90). MolNFT v1 #143927 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6BE1
- Type
- protein
- Length
- 1,995 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A
- UniProt
- E9QLC0
- Ligands
- PX4, NAG, BMA, NA, CL
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | 5-hydroxytryptamine receptor 3A | protein | 399 | 34% helix, 20% strand | E9QLC0 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, E, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 29 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
- NA · Sodium ion · metal
- CL · Chloride ion · ion · chains A, C, E
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 | 1089 | 0.90 | 0.92 | 127 | NA |
| 2 | 898 | 0.83 | 0.84 | 69 | CL |
| 3 | 454 | 0.82 | 0.89 | 58 | empty |
| 4 | 492 | 0.81 | 0.87 | 54 | empty |
| 5 | 265 | 0.80 | 0.92 | 58 | empty |
Interfaces
5 interfaces between chains.
- B–C · 3394 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 3377 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3351 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 3297 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 3208 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 5 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 6BE1 · Cryo-EM structure of serotonin receptor · 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 6BE1 · PDBe 6BE1 · UniProt E9QLC0
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