Complex of voltage-gated sodium channel navpas from american cockroach periplaneta americana bound with tetrodotoxin and DC1A

Structure

electron microscopy · 2 distinct chains · 60% helix, 4% strand (DSSP).

Ligands and binding sites

• 9SR · (1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5, 9,12,13,14-pentol (non-preferred name) · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
• NA · Sodium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1235 Ų buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

• 6A95 · Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta… · the same entry in another collection · chain A against A, TM-score 1.00
• D0E0C2 · AlphaFold monomer V2.0 prediction for sodium channel protein PAFPC1 (D0E0C2) · a predicted model of the same protein · chain A against A, TM-score 0.93
• P49126 · AlphaFold monomer V2.0 prediction for beta-diguetoxin-DC1A (P49126) · a predicted model of the same protein · chain B 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 D0E0C2
• Every structure of UniProt P49126
• Elsewhere: RCSB PDB 6A95 · PDBe 6A95 · UniProt D0E0C2 · UniProt P49126