MolNFT v1 · #190278 · protein
Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2
7WRF · Transient receptor potential cation channel subfamily M…: “Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2”. Electron microscopy, 3 ligands (KX7, CA, NA), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 7WRF
- Type
- protein
- Length
- 3,720 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 8
- UniProt
- Q8R4D5
- Ligands
- KX7, CA, NA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 8 | protein | 930 | 62% helix, 5% strand | Q8R4D5 |
Ligands and binding sites
- KX7 · Icilin · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 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 | 504 | 0.84 | 0.90 | 35 | NA |
| 2 | 920 | 0.79 | 0.81 | 74 | KX7 |
| 3 | 874 | 0.79 | 0.81 | 68 | KX7 |
| 4 | 868 | 0.79 | 0.81 | 76 | KX7 |
| 5 | 896 | 0.79 | 0.81 | 73 | KX7 |
Interfaces
6 interfaces between chains.
- B–C · 4051 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 4048 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 4047 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4038 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 55 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7WRF · Mouse TRPM8 in lipid nanodiscs in the presence of calcium, icilin and PI(4,5)P2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R4D5 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q8R4D5
- Elsewhere: RCSB PDB 7WRF · PDBe 7WRF · UniProt Q8R4D5
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