Research workbench
Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy
Analyse Structure of the capsaicin receptor, TRPV1, determined by single particle… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3J9J
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1
- UniProt
- O35433
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 1 | protein | 315 | 73% helix, 0% strand | O35433 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.86 | 0.96 | 32 | empty |
| 2 | 168 | 0.72 | 0.90 | 23 | empty |
| 3 | 328 | 0.71 | 0.84 | 45 | empty |
| 4 | 329 | 0.71 | 0.84 | 46 | empty |
| 5 | 384 | 0.68 | 0.80 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2023 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 2018 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 2015 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 2012 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 14 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3J9J · Structure of the capsaicin receptor, TRPV1, determined by single particle electron… · the same entry in another collection · chain A against A, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 O35433
- Elsewhere: RCSB PDB 3J9J · PDBe 3J9J · UniProt O35433
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