Research workbench
Cryo-EM structure of the TRPM8 ion channel in complex with high occupancy icilin, PI(4,5)P2, and calcium
Analyse Cryo-EM structure of the TRPM8 ion channel in complex with high occupancy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NR3
- Type
- protein
- Length
- 3,416 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
- KX7, KXP, CA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 1 distinct chain · 66% 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 | 854 | 66% helix, 4% strand | — |
Ligands and binding sites
- KX7 · Icilin · ligand · 4 copies · chains A, B, C, D
- 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
- 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 | 595 | 0.81 | 0.86 | 53 | KX7, CA |
| 2 | 762 | 0.80 | 0.84 | 69 | KX7, CA |
| 3 | 666 | 0.80 | 0.84 | 56 | KX7, CA |
| 4 | 731 | 0.79 | 0.83 | 68 | KX7, CA |
| 5 | 914 | 0.79 | 0.81 | 106 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1955 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1952 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1946 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 1941 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6NR3 · Cryo-EM structure of the TRPM8 ion channel in complex with high occupancy icilin… · 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 6NR3 · PDBe 6NR3
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