MolNFT v1 · #188832 · protein
Cryo-EM structure of TRPV3 in complex with the anesthetic dyclonine
7UGG · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of TRPV3 in complex with the anesthetic dyclonine”. Electron microscopy, 3 ligands (POV, N8R, NA), 20 pockets (best druggability 0.84). MolNFT v1 #188832…
- PDB
- 7UGG
- Type
- protein
- Length
- 2,480 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 3
- UniProt
- Q8K424
- Ligands
- POV, N8R, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 54% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 3 | protein | 620 | 54% helix, 5% strand | Q8K424 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 24 copies · chains A, B, D, C
- N8R · Dyclonine · ligand · 4 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains A, 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 | 949 | 0.84 | 0.84 | 75 | N8R, NA |
| 2 | 787 | 0.81 | 0.84 | 78 | POV |
| 3 | 991 | 0.81 | 0.82 | 97 | POV |
| 4 | 978 | 0.81 | 0.82 | 81 | POV |
| 5 | 1061 | 0.80 | 0.81 | 96 | POV |
Interfaces
4 interfaces between chains.
- C–D · 2590 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2574 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 2571 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 2554 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7UGG · Cryo-EM structure of TRPV3 in complex with the anesthetic dyclonine · the same entry in another collection · chain A against A, TM-score 1.00
- Q8K424 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q8K424
- Elsewhere: RCSB PDB 7UGG · PDBe 7UGG · UniProt Q8K424
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