Research workbench
Structure of the TRPM8 cold receptor by single particle electron cryo- microscopy, calcium-bound state
Analyse Structure of the TRPM8 cold receptor by single particle electron cryo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O77
- Type
- protein
- Length
- 3,488 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, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 58% 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 | 872 | 58% helix, 5% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 12 copies · chains A, D, B, C
- CA · Calcium 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 | 1001 | 0.84 | 0.85 | 76 | empty |
| 2 | 1013 | 0.77 | 0.79 | 89 | empty |
| 3 | 105 | 0.77 | 0.96 | 19 | empty |
| 4 | 968 | 0.77 | 0.79 | 90 | empty |
| 5 | 844 | 0.77 | 0.80 | 73 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4237 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 4231 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 4230 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 4228 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6O77 · 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 6O77 · PDBe 6O77
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