Research workbench
Structure of the TRPM8 cold receptor by single particle electron cryo- microscopy, tc-I 2014-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
- 6O72
- Type
- protein
- Length
- 3,432 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, 9PE, T14, NA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 59% 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 | 858 | 59% helix, 5% strand | — |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A, B, C, D
- 9PE · (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate · ligand · 4 copies · chains A, D, B, C
- T14 · 3-{7-(trifluoromethyl)-5-[2-(trifluoromethyl)phenyl]-1H-benzimidazol-2-yl}-1-oxa-2-azaspiro[4.5]dec-2-ene · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- UND · Undecane · additive · 8 copies · chains A, D, B, C
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 | 670 | 0.80 | 0.84 | 54 | Y01, T14 |
| 2 | 952 | 0.80 | 0.81 | 91 | Y01, T14 |
| 3 | 770 | 0.79 | 0.83 | 65 | Y01, T14 |
| 4 | 1050 | 0.79 | 0.81 | 86 | empty |
| 5 | 1187 | 0.79 | 0.81 | 108 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4315 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 4307 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 4302 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 4300 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6O72 · Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, TC-I… · 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 6O72 · PDBe 6O72
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