Cryo-EM structure of the full-length TRPV1 with rtx at 25 degrees celsius, in an open state, class B

Structure

electron microscopy · 1 distinct chain · 59% 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 · 8 copies · chains A, D, B, C
• 6EU · resiniferatoxin · ligand · 4 copies · chains A, C, B, D
• LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 4 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.

Interfaces

4 interfaces between chains.

• A–C · 2209 Ų buried · 10 hydrogen bonds · protein-protein
• A–D · 2195 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 2188 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 2186 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 7RQY · Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an open… · 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 0.93

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 7RQY · PDBe 7RQY · UniProt O35433