SMTL ID : 7xsu.1

Cardiac sodium channel in complex with LqhIII

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

NAG.1: 3 residues within 4Å: Chain A: N.1063, N.1064 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1063, A:N.1064 NAG.2: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) NAG.3: 2 residues within 4Å: Chain A: N.319, W.1368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.319 NAG.4: 7 residues within 4Å: Chain A: H.279, N.329, R.341, C.342, L.343, K.344 Ligands: NAG.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.344 Hydrogen bonds: A:N.329, A:R.341, A:R.341 NAG.5: 3 residues within 4Å: Chain A: R.341 Ligands: NAG.4, BMA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.341

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.6: 1 residues within 4Å: Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

6 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.7: 8 residues within 4Å: Chain A: M.255, V.259, A.360, W.361, F.363, L.364, L.722, L.726 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.259, A:F.363, A:L.726 6OU.8: 5 residues within 4Å: Chain A: F.222, L.664, S.716, S.719 Ligands: 6OU.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.222, A:L.664 Hydrogen bonds: A:S.719 6OU.9: 2 residues within 4Å: Chain A: S.719 Ligands: 6OU.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.719 6OU.10: 7 residues within 4Å: Chain A: W.1029, G.1090, A.1091, A.1430, I.1433, T.1437, I.1441 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.1029, A:A.1430, A:I.1433, A:I.1441 6OU.11: 4 residues within 4Å: Chain A: I.633, G.637, F.1140 Ligands: 6OU.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.633, A:F.1140, A:F.1140 6OU.12: 8 residues within 4Å: Chain A: W.585, F.588, F.620, I.633, I.1031, F.1032, M.1035 Ligands: 6OU.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.620, A:I.1031, A:F.1032

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

9Z9.13: 8 residues within 4Å: Chain A: L.410, V.413, Y.417, L.741, I.1150, I.1154, I.1455, L.1456 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.410, A:V.413, A:Y.417, A:L.741, A:I.1150, A:I.1455, A:I.1455, A:L.1456

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, D. et al., Structural Basis for Nav1.5 Opening Modulated by a Gating Modifier Toxin. To Be Published

Release Date

2023-11-29

Peptides

Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein: A
Alpha-like toxin Lqh3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein

Alpha-like toxin Lqh3

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