Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60, conformation 2

Structure

electron microscopy · 1 distinct chain · 61% helix, 4% strand (DSSP).

Ligands and binding sites

• PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 8 copies · chains A, B, D, C
• 0IG · ~{N}-[4-[4-[(azanylidene-$L^{4}-azanylidene) amino]phenyl]-1,3-thiazol-2-yl]-2-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]ethanamide · ligand · 4 copies · chains A, B, C, D
• IHP · Inositol hexakisphosphate · ligand · 4 copies · chains A, B, C, D
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
• CA · Calcium ion · metal · 5 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, 17 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 3585 Ų buried · 15 hydrogen bonds · protein-protein
• A–D · 3518 Ų buried · 15 hydrogen bonds · protein-protein
• C–D · 3491 Ų buried · 16 hydrogen bonds · protein-protein
• A–B · 3489 Ų buried · 12 hydrogen bonds · protein-protein
• B–D · 467 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan (N-glycosylation).

Compared structures

• 7OR0 · Cryo-EM structure of the human TRPA1 ion channel in complex with the antagonist 3-60… · the same entry in another collection · chain A against A, TM-score 1.00
• O75762 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.86

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 O75762
• Elsewhere: RCSB PDB 7OR0 · PDBe 7OR0 · UniProt O75762