Research workbench
X-ray structure of the mouse serotonin 5-HT3 receptor
Analyse X-ray structure of the mouse serotonin 5-HT3 receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PIR
- Type
- protein
- Length
- 2,535 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-hydroxytryptamine receptor 3A; VHH15
- UniProt
- P23979
- Ligands
- NAG, BMA, CL, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | 5-hydroxytryptamine receptor 3A | protein | 383 | 40% helix, 25% strand | P23979 |
| C, D | 5-hydroxytryptamine receptor 3A | protein | 384 | 40% helix, 26% strand | P23979 |
| F | VHH15 | protein | 122 | 2% helix, 58% strand | — |
| G, H, I, J | VHH15 | protein | 124 | 2% helix, 59% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, B, C, D, E
- BMA · beta-D-mannopyranose · sugar · 5 copies
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 3 copies · chains B, C, D, E, H
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 | 900 | 0.83 | 0.84 | 82 | empty |
| 2 | 338 | 0.81 | 0.90 | 56 | empty |
| 3 | 802 | 0.80 | 0.83 | 77 | empty |
| 4 | 902 | 0.80 | 0.82 | 82 | empty |
| 5 | 894 | 0.80 | 0.82 | 76 | empty |
Interfaces
15 interfaces between chains.
- B–C · 3191 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 3174 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 3165 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3138 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 3137 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
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 4PIR · PDBe 4PIR · UniProt P23979
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