Research workbench
Cryo-EM structure of human TRPV3 determined in lipid nanodisc
Analyse Cryo-EM structure of human TRPV3 determined in lipid nanodisc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6UW4
- Type
- protein
- Length
- 2,412 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
- Q8NET8
- Ligands
- 6OU, NA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 56% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 3 | protein | 603 | 56% helix, 4% strand | Q8NET8 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 20 copies · chains A, D, B, C
- NA · Sodium ion · metal · 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 | 432 | 0.86 | 0.94 | 40 | NA |
| 2 | 217 | 0.79 | 0.93 | 21 | empty |
| 3 | 763 | 0.77 | 0.81 | 66 | 6OU |
| 4 | 833 | 0.77 | 0.80 | 70 | 6OU |
| 5 | 748 | 0.77 | 0.81 | 67 | 6OU |
Interfaces
6 interfaces between chains.
- A–D · 2864 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 2863 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 2857 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2857 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6UW4 · Cryo-EM structure of human TRPV3 determined in lipid nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NET8 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8NET8
- Elsewhere: RCSB PDB 6UW4 · PDBe 6UW4 · UniProt Q8NET8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.