SMTL ID : 7k18.1

Cardiac Sodium channel with toxin bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.1063, N.1064, S.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.1072, G.1075, L.1077, Y.1078, W.1079, P.1409 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1409

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

NAG-NAG-BMA.2: 5 residues within 4Å: Chain A: H.279, N.329, R.341, C.342, L.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.341, A:R.341

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

NAG.4: 3 residues within 4Å: Chain A: N.319, W.1368, D.1374 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.1374 Hydrogen bonds: A:N.319, A:D.1374

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

6OU.5: 6 residues within 4Å: Chain A: A.360, W.361, F.363, F.367, Q.718, L.722 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.361, A:F.363, A:F.363, A:F.367, A:L.722 Hydrogen bonds: A:Q.718 6OU.6: 6 residues within 4Å: Chain A: A.218, G.717, Q.718, S.719, L.720 Ligands: 6OU.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.218, A:L.720 Hydrogen bonds: A:Q.718 6OU.7: 2 residues within 4Å: Chain A: S.719 Ligands: 6OU.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.719 6OU.8: 1 residues within 4Å: Chain A: V.1231 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.1231 6OU.9: 8 residues within 4Å: Chain A: L.1022, G.1090, A.1091, A.1430, I.1433, T.1437, T.1438, I.1441 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1022, A:A.1430, A:I.1433, A:I.1441 6OU.10: 7 residues within 4Å: Chain A: S.985, T.988, L.992, L.995, N.1362, A.1430, L.1434 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.995, A:A.1430, A:L.1434 Hydrogen bonds: A:A.1361 6OU.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 6OU.12: 5 residues within 4Å: Chain A: L.900, A.907, F.1001, F.1349, F.1381 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.900, A:A.907, A:F.1001, A:F.1349 6OU.13: 5 residues within 4Å: Chain A: A.150, Q.151, H.152, F.690, Y.1129 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.150 Hydrogen bonds: A:Q.151, A:H.152, A:Y.1129 Salt bridges: A:H.152 6OU.14: 4 residues within 4Å: Chain A: I.633, G.637, F.1140 Ligands: 6OU.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1140 6OU.15: 5 residues within 4Å: Chain A: W.585, F.588, F.620, F.1032 Ligands: 6OU.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.585, A:F.620, A:F.620, A:F.1032

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, D. et al., Structural basis for voltage-sensor trapping of the cardiac sodium channel by a deathstalker scorpion toxin. Nat Commun (2021)

Release Date

2021-01-20

Peptides

Sodium channel protein type 5 subunit alpha, Enhanced Green fluorescent 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, Enhanced Green fluorescent protein

Alpha-like toxin Lqh3

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