Research workbench
Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees celsius
Analyse Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees celsius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MIK
- Type
- protein
- Length
- 2,560 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, 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 | 640 | 54% helix, 5% strand | Q8K424 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 36 copies · chains A, D, B, C
- NA · Sodium ion · metal · 4 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 | 498 | 0.84 | 0.90 | 29 | NA |
| 2 | 1069 | 0.79 | 0.80 | 78 | POV |
| 3 | 1086 | 0.78 | 0.80 | 80 | POV |
| 4 | 1080 | 0.78 | 0.80 | 88 | POV |
| 5 | 1115 | 0.78 | 0.79 | 87 | POV |
Interfaces
6 interfaces between chains.
- B–C · 2926 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 2918 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 2905 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2903 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7MIK · Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees Celsius · 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 0.96
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 Q8K424
- Elsewhere: RCSB PDB 7MIK · PDBe 7MIK · UniProt Q8K424
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