Cryo-EM structure of minimal TRPV1 with 1 perturbed pi

Structure

electron microscopy · 1 distinct chain · 57% helix, 4% strand (DSSP).

Ligands and binding sites

• XJ7 · (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2r,3s,4s,5r, 6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate · ligand · 4 copies · chains A, D, C, B
• 6IY · (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate · ligand · 4 copies · chains A, D, B, C
• NA · Sodium ion · metal · 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, 14 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 2695 Ų buried · 12 hydrogen bonds · protein-protein
• A–D · 2687 Ų buried · 10 hydrogen bonds · protein-protein
• B–C · 2672 Ų buried · 8 hydrogen bonds · protein-protein
• D–C · 2646 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 7MZ6 · Cryo-EM structure of minimal TRPV1 with 1 perturbed PI · 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 0.97

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 7MZ6 · PDBe 7MZ6 · UniProt O35433