Research workbench
Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees celsius
Analyse Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees celsius in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LPA
- Type
- protein
- Length
- 2,392 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, 4DY, YFP, NA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 1 distinct chain · 58% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 1 | protein | 598 | 58% helix, 5% 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 · 12 copies · chains A, D, B, C
- LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, B, C, D
- 4DY · (6E)-N-(4-hydroxy-3-methoxybenzyl)-8-methylnon-6-enamide · ligand · 4 copies · chains A, D, B, C
- YFP · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol · ligand · 4 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 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 | 249 | 0.83 | 0.95 | 32 | NA |
| 2 | 631 | 0.77 | 0.83 | 59 | LBN |
| 3 | 585 | 0.77 | 0.83 | 63 | LBN |
| 4 | 526 | 0.76 | 0.84 | 49 | LBN |
| 5 | 549 | 0.76 | 0.83 | 62 | LBN |
Interfaces
6 interfaces between chains.
- A–B · 2534 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 2526 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 2525 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 2520 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LPA · Cryo-EM structure of full-length TRPV1 with capsaicin at 4 degrees Celsius · the same entry in another collection · chain A against A, TM-score 1.00
- O35433 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 7LPA · PDBe 7LPA · UniProt O35433
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