MolNFT v1 · #146890 · protein
Cryo-EM structure of mouse TRPV3-Y564A in complex with 2- aminoethoxydiphenyl borate (2-apb)
6DVZ · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of mouse TRPV3-Y564A in complex with 2- aminoethoxydiphenyl borate (2-apb)”. Electron microscopy, 1 ligand (FZ4), 20 pockets (best druggability 0.84).…
- PDB
- 6DVZ
- Type
- protein
- Length
- 2,572 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 0.84
Structure
electron microscopy · 1 distinct chain · 49% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 3 | protein | 643 | 49% helix, 2% strand | Q8K424 |
Ligands and binding sites
- FZ4 · 2-aminoethyl diphenylborinate · ligand · 12 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 | 914 | 0.84 | 0.86 | 69 | empty |
| 2 | 856 | 0.73 | 0.78 | 105 | empty |
| 3 | 744 | 0.73 | 0.78 | 90 | empty |
| 4 | 421 | 0.72 | 0.82 | 43 | FZ4 |
| 5 | 310 | 0.72 | 0.84 | 26 | FZ4 |
Interfaces
4 interfaces between chains.
- A–B · 2912 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 2910 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 2906 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2900 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 6DVZ · Cryo-EM structure of mouse TRPV3-Y564A in complex with 2-Aminoethoxydiphenyl borate… · 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 0.95
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 Q8K424
- Elsewhere: RCSB PDB 6DVZ · PDBe 6DVZ · UniProt Q8K424
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