Research workbench
Cryo-EM structure of the TRPM8 ion channel in complex with the menthol analog ws-12 and PI(4,5)P2
Analyse Cryo-EM structure of the TRPM8 ion channel in complex with the menthol analog… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NR2
- Type
- protein
- Length
- 3,436 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
- KXP, KXS
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 65% 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 | 859 | 65% helix, 4% strand | — |
Ligands and binding sites
- KXP · (2S)-1-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy) propan-2-yl icosa-5,8,11,14-tetraenoate · ligand · 4 copies · chains A, D, B, C
- KXS · (1R,2S,5R)-N-(4-methoxyphenyl)-5-methyl-2-(propan-2-yl)cyclohexane-1-carboxamide · ligand · 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 | 943 | 0.80 | 0.82 | 73 | KXS |
| 2 | 899 | 0.80 | 0.82 | 66 | KXS |
| 3 | 1048 | 0.80 | 0.81 | 89 | KXS |
| 4 | 847 | 0.80 | 0.82 | 61 | KXS |
| 5 | 886 | 0.75 | 0.78 | 114 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2732 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 2730 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 2715 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 2714 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6NR2 · Cryo-EM structure of the TRPM8 ion channel in complex with the menthol analog WS-12 and… · 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 6NR2 · PDBe 6NR2
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