Research workbench
Cbd-bound full-length rat TRPV2 in nanodiscs, state 1
Analyse Cbd-bound full-length rat TRPV2 in nanodiscs, state 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8A
- Type
- protein
- Length
- 2,468 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 2
- UniProt
- Q9WUD2
- Ligands
- P0T
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 53% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 2 | protein | 617 | 53% helix, 5% strand | Q9WUD2 |
Ligands and binding sites
- P0T · cannabidiol · ligand · 4 copies · chains A, B, D, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.84 | 0.85 | 48 | empty |
| 2 | 275 | 0.77 | 0.89 | 31 | empty |
| 3 | 296 | 0.77 | 0.88 | 32 | empty |
| 4 | 297 | 0.77 | 0.88 | 30 | empty |
| 5 | 1114 | 0.77 | 0.78 | 96 | P0T |
Interfaces
6 interfaces between chains.
- C–D · 3159 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 3150 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 3150 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 3133 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6U8A · CBD-bound full-length rat TRPV2 in nanodiscs, state 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WUD2 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9WUD2
- Elsewhere: RCSB PDB 6U8A · PDBe 6U8A · UniProt Q9WUD2
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