MolNFT v1 · #158842 · protein
Structure of the TRPM8 cold receptor by single particle electron cryo- microscopy, ligand-free state
6O6A · Transient receptor potential cation channel subfamily M…: “Structure of the TRPM8 cold receptor by single particle electron cryo- microscopy, ligand-free state”. Electron microscopy, 2 ligands (Y01, NA), 20 pockets (best…
- PDB
- 6O6A
- Type
- protein
- Length
- 3,312 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily M member 8
- Ligands
- Y01, NA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily M member 8 | protein | 828 | 57% helix, 4% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A, B, C, D
- 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 | 133 | 0.80 | 0.96 | 22 | empty |
| 2 | 726 | 0.79 | 0.83 | 68 | Y01 |
| 3 | 775 | 0.79 | 0.82 | 82 | Y01 |
| 4 | 818 | 0.79 | 0.82 | 71 | Y01 |
| 5 | 788 | 0.78 | 0.82 | 78 | Y01 |
Interfaces
6 interfaces between chains.
- A–B · 4285 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 4256 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4250 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 4196 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6O6A · Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6O6A · PDBe 6O6A
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