Research workbench
Structure of the TRPM8 cold receptor by single particle electron cryo-microscopy, AMTB-bound state
Analyse Structure of the TRPM8 cold receptor by single particle electron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O6R
- Type
- protein
- Length
- 3,332 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Parus major
- Molecule
- Transient receptor potential cation channel subfamily M member 8
- Ligands
- Y01, 9PE, LQ7, NA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.2 · 1 distinct chain · 53% 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 | 833 | 53% helix, 4% 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
- LQ7 · N-(3-aminopropyl)-2-[(3-methylphenyl)methoxy]-N-[(thiophen-2-yl)methyl]benzamide · 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 | 568 | 0.82 | 0.87 | 58 | empty |
| 2 | 988 | 0.80 | 0.81 | 84 | Y01, LQ7 |
| 3 | 1045 | 0.79 | 0.81 | 88 | Y01, LQ7 |
| 4 | 1080 | 0.79 | 0.80 | 90 | Y01, LQ7 |
| 5 | 1068 | 0.79 | 0.80 | 89 | Y01, LQ7 |
Interfaces
6 interfaces between chains.
- A–B · 4298 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4269 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 4221 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 4191 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct).
Compared structures
- 6O6R · 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 6O6R · PDBe 6O6R
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