Research workbench
Cryo-EM structure of full-length TRPV1 at 48 degrees celsius
Analyse Cryo-EM structure of full-length TRPV1 at 48 degrees celsius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LPC
- Type
- protein
- Length
- 1,816 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 1
- UniProt
- O35433
- Ligands
- 6OU, LBN, YFP, T7X
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 61% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, B, D | Transient receptor potential cation channel subfamily V member 1 | protein | 454 | 61% helix, 7% strand | O35433 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 24 copies · chains C, B, D, A
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains C, A, B, D
- YFP · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol · ligand · 4 copies · chains C, B, A, D
- T7X · Phosphatidylinositol · ligand · 4 copies · chains C, B, A, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.84 | 0.96 | 31 | empty |
| 2 | 966 | 0.81 | 0.82 | 83 | T7X, LBN |
| 3 | 952 | 0.80 | 0.82 | 80 | T7X, LBN |
| 4 | 956 | 0.80 | 0.81 | 83 | T7X, LBN |
| 5 | 1057 | 0.79 | 0.81 | 90 | T7X, LBN |
Interfaces
6 interfaces between chains.
- C–B · 2173 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 2167 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 2155 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 2133 Ų buried · 4 hydrogen bonds · protein-protein
- C–A · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LPC · Cryo-EM structure of full-length TRPV1 at 48 degrees Celsius · the same entry in another collection · chain C against C, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain C against A, TM-score 0.96
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 O35433
- Elsewhere: RCSB PDB 7LPC · PDBe 7LPC · UniProt O35433
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