Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist bitc

Structure

electron microscopy · 1 distinct chain · 63% helix, 3% 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 · 20 copies · chains A, D, B, C
• 9BE · N-benzylthioformamide · ligand · 4 copies · chains A, D, B, C
• LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B, D, C
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 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, 19 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 3500 Ų buried · 13 hydrogen bonds · protein-protein
• A–D · 3498 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 3489 Ų buried · 15 hydrogen bonds · protein-protein
• D–C · 3482 Ų buried · 15 hydrogen bonds · protein-protein
• D–B · 458 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 glycan (covalent ligand, N-glycosylation).

Compared structures

• 6PQP · Cryo-EM structure of the human TRPA1 ion channel in complex with the covalent agonist BITC · 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 0.85

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 6PQP · PDBe 6PQP · UniProt O75762