Research workbench
Cryo-EM structure of mouse TRPV3 in complex with 2-aminoethoxydiphenyl borate (2-apb)
Analyse Cryo-EM structure of mouse TRPV3 in complex with 2-aminoethoxydiphenyl borate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DVY
- Type
- protein
- Length
- 2,564 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 3
- UniProt
- Q8K424
- Ligands
- FZ4
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 52% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 3 | protein | 641 | 52% helix, 3% strand | Q8K424 |
Ligands and binding sites
- FZ4 · 2-aminoethyl diphenylborinate · ligand · 8 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 | 1103 | 0.86 | 0.86 | 93 | empty |
| 2 | 247 | 0.72 | 0.86 | 27 | FZ4 |
| 3 | 244 | 0.71 | 0.86 | 28 | FZ4 |
| 4 | 259 | 0.70 | 0.84 | 27 | FZ4 |
| 5 | 246 | 0.69 | 0.85 | 30 | FZ4 |
Interfaces
6 interfaces between chains.
- A–D · 3032 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 3031 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 3022 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 3018 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6DVY · Cryo-EM structure of mouse TRPV3 in complex with 2-Aminoethoxydiphenyl borate (2-APB) · the same entry in another collection · chain A against A, TM-score 1.00
- Q8K424 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q8K424
- Elsewhere: RCSB PDB 6DVY · PDBe 6DVY · UniProt Q8K424
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