SMTL ID : 9ith.1

Nav1.5 in complex with TTX

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

9 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.326, E.380 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.380 NAG.2: 1 residues within 4Å: Chain A: N.331 No protein-ligand interaction detected (PLIP) NAG.3: 1 residues within 4Å: Chain A: N.334 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.361, D.1733 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.1733 Hydrogen bonds: A:N.361 NAG.5: 5 residues within 4Å: Chain A: H.321, N.371, R.383, C.384, L.385 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.321, A:N.371, A:R.383, A:C.384 NAG.6: 5 residues within 4Å: Chain A: N.1408, T.1410, E.1411, L.1416, E.1435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.1411 NAG.7: 2 residues within 4Å: Chain A: N.1417, T.1419 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.1422, N.1423 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.1423 Hydrogen bonds: A:N.1422 NAG.9: 6 residues within 4Å: Chain A: E.1428, N.1431, G.1434, L.1436, Y.1437, W.1438 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1438 Hydrogen bonds: A:L.1436

1 x 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)(Non-covalent)

9SR.10: 13 residues within 4Å: Chain A: D.415, C.416, E.418, E.941, E.944, F.1461, K.1462, G.1463, W.1464, M.1465, D.1466, G.1755, D.1757 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.415, A:D.415, A:C.416, A:E.944, A:G.1463, A:W.1464, A:M.1465, A:D.1466, A:G.1755, A:D.1757 Salt bridges: A:E.418, A:E.941, A:E.944

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.11: 13 residues within 4Å: Chain A: L.452, A.456, F.977, L.978, L.981, L.982, L.1505, I.1509, I.1513, N.1517, Y.1810, I.1811, I.1814 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.456, A:F.977, A:L.978, A:L.981, A:L.982, A:I.1513, A:Y.1810, A:I.1811, A:I.1814, A:I.1814 Hydrogen bonds: A:N.1517

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, T. et al., Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na v channels. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-08-20

Peptides

Sodium channel protein type 5 subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 5 subunit alpha

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