Cryo-EM structure of the full-length TRPV1 with rtx at 4 degrees celsius, in an intermediate-closed state, class II

Structure

electron microscopy · 1 distinct chain · 53% helix, 4% 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 · 4 copies · chains A, C, D, B
• 6EU · resiniferatoxin · ligand · 4 copies · chains A, D, C, B
• NA · Sodium ion · metal · 2 copies · chains A, C, D, B

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–B · 2476 Ų buried · 8 hydrogen bonds · protein-protein
• A–D · 2475 Ų buried · 7 hydrogen bonds · protein-protein
• C–B · 2474 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 2472 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 7RQV · Cryo-EM structure of the full-length TRPV1 with RTx at 4 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 0.96

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 7RQV · PDBe 7RQV · UniProt O35433