Research workbench
Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees celsius, in an open state, class 1
Analyse Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees celsius, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LPE
- Type
- protein
- Length
- 1,944 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
- LBN, 6OU, 4DY
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A, D | Transient receptor potential cation channel subfamily V member 1 | protein | 486 | 65% helix, 5% strand | O35433 |
Ligands and binding sites
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains C, B, A, D
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 4 copies · chains C, D, B, A
- 4DY · (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide · ligand · 4 copies · chains C, D, B, A
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 | 809 | 0.83 | 0.85 | 63 | empty |
| 2 | 1002 | 0.80 | 0.81 | 119 | empty |
| 3 | 1020 | 0.77 | 0.79 | 111 | empty |
| 4 | 996 | 0.77 | 0.79 | 110 | empty |
| 5 | 1040 | 0.77 | 0.79 | 108 | empty |
Interfaces
4 interfaces between chains.
- B–A · 1960 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 1958 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 1954 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1951 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LPE · Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an open… · 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 0.94
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 7LPE · PDBe 7LPE · UniProt O35433
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