Structure of the human voltage-gated sodium channel NAV1.4 in complex with BETA1

Structure

electron microscopy · 2 distinct chains · 60% helix, 5% 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 · 6 copies · chains A
• 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 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, 16 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 2021 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

• 6AGF · Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1 · the same entry in another collection · chain A against A, TM-score 1.00
• P35499 · AlphaFold monomer V2.0 prediction for sodium channel protein type 4 subunit alpha (P35499) · a predicted model of the same protein · chain A against A, TM-score 0.98
• Q07699 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-1 (Q07699) · a predicted model of the same protein · chain B against A, TM-score 0.90

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 P35499
• Every structure of UniProt Q07699
• Elsewhere: RCSB PDB 6AGF · PDBe 6AGF · UniProt P35499 · UniProt Q07699