SMTL ID : 6uz3.1

Cardiac sodium channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

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, E.1067 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 No protein-ligand interaction detected (PLIP)

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: C.327, N.329, C.342, L.343, K.344 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.319, L.325 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.325 Hydrogen bonds: A:N.319 NAG.5: 6 residues within 4Å: Chain A: N.284, P.337, E.338, G.339, Y.340, R.341 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.339, A:Y.340, A:R.341

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

9Z9.6: 9 residues within 4Å: Chain A: D.332, K.388, I.389, M.391, M.395, A.1382, M.1385, L.1386 Ligands: 6OU.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.1382, A:L.1386 9Z9.7: 4 residues within 4Å: Chain A: L.1224, K.1240, L.1244, I.1247 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1224, A:K.1240, A:L.1244, A:I.1247 9Z9.8: 8 residues within 4Å: Chain A: L.536, H.542, L.1030, N.1088, V.1089, G.1090 Ligands: 9Z9.9, 6OU.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.536, A:H.542, A:N.1088 9Z9.9: 7 residues within 4Å: Chain A: L.622, S.625, W.626, P.627, L.1023, I.1027 Ligands: 9Z9.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.622, A:L.622, A:W.626, A:W.626, A:L.1023, A:L.1023 9Z9.10: 10 residues within 4Å: Chain A: M.1035, L.1039, N.1127, Y.1129, M.1130, I.1132, Y.1133, V.1136 Ligands: 6OU.20, 6OU.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1039, A:I.1132, A:Y.1133, A:V.1136

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

6OU.11: 6 residues within 4Å: Chain A: S.358, W.361, L.364, Q.718, L.722, L.723 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.361, A:L.364, A:L.723 Hydrogen bonds: A:S.358, A:Q.718 6OU.12: 3 residues within 4Å: Chain A: S.719, L.720 Ligands: 6OU.13 No protein-ligand interaction detected (PLIP) 6OU.13: 3 residues within 4Å: Chain A: S.719, L.723 Ligands: 6OU.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.723 6OU.14: 1 residues within 4Å: Chain A: F.359 No protein-ligand interaction detected (PLIP) 6OU.15: 8 residues within 4Å: Chain A: L.1022, G.1090, A.1091, A.1430, I.1433, L.1434, I.1441 Ligands: 6OU.16 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1022, A:L.1434, A:I.1441 6OU.16: 7 residues within 4Å: Chain A: L.992, L.995, F.1358, A.1361, A.1430, L.1434 Ligands: 6OU.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.992, A:L.995, A:F.1358, A:A.1430, A:L.1434 Hydrogen bonds: A:A.1361 6OU.17: 2 residues within 4Å: Chain A: L.540 Ligands: 9Z9.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.540 6OU.18: 7 residues within 4Å: Chain A: A.907, F.908, F.1001, F.1349, F.1353, F.1381 Ligands: 9Z9.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1001, A:F.1353 6OU.19: 6 residues within 4Å: Chain A: V.147, A.150, H.152, D.689, F.690, Y.1129 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1129, A:Y.1129 6OU.20: 5 residues within 4Å: Chain A: W.585, I.633, K.634 Ligands: 9Z9.10, 6OU.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.633 Salt bridges: A:K.634 6OU.21: 5 residues within 4Å: Chain A: W.585, F.588, F.620 Ligands: 9Z9.10, 6OU.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.585

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, D. et al., Structure of the Cardiac Sodium Channel. Cell (2020)

Release Date

2020-01-01

Peptides

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

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