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Voltage-gated sodium channel BETA3 subunit ig domain

Analyse Voltage-gated sodium channel BETA3 subunit ig domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4L1D
Type
protein
Length
332 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Sodium channel subunit beta-3
UniProt
Q9NY72
Pockets
5 · best druggability 0.70

Structure

x-ray diffraction · 3 distinct chains · 3% helix, 47% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ASodium channel subunit beta-3protein1133% helix, 48% strandQ9NY72
BSodium channel subunit beta-3protein1103% helix, 46% strandQ9NY72
CSodium channel subunit beta-3protein1093% helix, 46% strandQ9NY72

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
12180.700.8744empty
22530.540.7636empty
32520.530.7629empty
41320.500.8019empty
5610.280.7414empty

Interfaces

3 interfaces between chains.

  • B–C · 471 Ų buried · 0 hydrogen bonds · protein-protein
  • A–B · 443 Ų buried · 0 hydrogen bonds · protein-protein
  • A–C · 439 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

  • 4L1D · Voltage-gated sodium channel beta3 subunit Ig domain · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9NY72 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-3 (Q9NY72) · a predicted model of the same protein · chain C against A, TM-score 0.98

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