SMTL ID : 8vqc.1

Structure of the voltage-gated sodium channel NavPas from American Cockroach Periplaneta Americana in complex with scorpion alpha-toxin LqhaIT

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- BMA- BMA- BMA- BMA: beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA-BMA-BMA.1: 12 residues within 4Å: Chain A: D.346, W.349, N.373, T.385, C.386, L.387, Q.388 Chain B: Y.11, N.55, I.58, V.60, R.65 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.55, B:Y.11 Hydrophobic interactions: A:T.385

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG.2: 2 residues within 4Å: Chain A: H.1075, N.1077 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: E.1057, N.1058 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.355, H.358 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.343 No protein-ligand interaction detected (PLIP)

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.6: 3 residues within 4Å: Chain A: W.341, R.348, N.351 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.1071 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Phulera, S. et al., Scorpion alpha-toxin Lqh alpha IT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels. Structure (2024)

Release Date

2024-09-04

Peptides

Sodium channel protein PaFPC1: A
Alpha-insect toxin LqhaIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein PaFPC1

Alpha-insect toxin LqhaIT

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