Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees celsius, in an intermediate state, class 2

Structure

electron microscopy · 1 distinct chain · 64% helix, 5% strand (DSSP).

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

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.

Interfaces

5 interfaces between chains.

• A–D · 2337 Ų buried · 6 hydrogen bonds · protein-protein
• C–D · 2332 Ų buried · 6 hydrogen bonds · protein-protein
• B–C · 2330 Ų buried · 6 hydrogen bonds · protein-protein
• A–B · 2325 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 7LPD · Cryo-EM structure of full-length TRPV1 with capsaicin at 48 degrees Celsius, in an… · 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 0.95

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 O35433
• Elsewhere: RCSB PDB 7LPD · PDBe 7LPD · UniProt O35433