SMTL ID : 8f6p.1

Rat Cardiac Sodium Channel with Ranolazine Bound

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(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 11 residues within 4Å: Chain A: C.1068, E.1069, N.1072, G.1075, L.1077, Y.1078, W.1079, P.1409 Ligands: BMA.6, BMA.8, BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.1063, N.1064, S.1066, E.1067, E.1120 No protein-ligand interaction detected (PLIP)

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)(Non-functional Binders)

NAG.3: 5 residues within 4Å: Chain A: N.284, E.338, G.339, Y.340, R.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.338 NAG.4: 7 residues within 4Å: Chain A: H.279, N.329, R.341, C.342, L.343, K.344 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.279, A:R.341 NAG.5: 4 residues within 4Å: Chain A: R.341, L.343 Ligands: NAG.4, NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.341 NAG.7: 8 residues within 4Å: Chain A: N.1049, T.1051, E.1052, F.1071, V.1073, T.1074, E.1076, L.1077 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1077 Hydrogen bonds: A:N.1049 NAG.10: 5 residues within 4Å: Chain A: L.681, N.1058, Y.1059, T.1060, W.1124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.1060, A:T.1060 NAG.11: 6 residues within 4Å: Chain A: N.319, L.325, R.384, W.1368, D.1373, D.1374 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.319 Hydrogen bonds: A:N.319, A:D.1374, A:D.1374 NAG.12: 1 residues within 4Å: Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

3 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.6: 5 residues within 4Å: Chain A: G.1408, P.1409, P.1414 Ligands: NAG-NAG.1, BMA.8 No protein-ligand interaction detected (PLIP) BMA.8: 8 residues within 4Å: Chain A: G.1408, P.1409, D.1413, P.1414, N.1415 Ligands: NAG-NAG.1, BMA.6, BMA.9 No protein-ligand interaction detected (PLIP) BMA.9: 8 residues within 4Å: Chain A: Y.1078, P.1409, P.1410, Y.1411, C.1412, D.1413 Ligands: NAG-NAG.1, BMA.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1078, A:P.1410

1 x XHO: (R)-ranolazine(Non-covalent)

XHO.13: 24 residues within 4Å: Chain A: M.370, T.371, Q.372, S.402, F.403, V.406, C.702, G.703, M.729, N.733, A.1100, T.1101, F.1102, K.1103, L.1146, T.1392, T.1393, S.1394, I.1440, S.1443, F.1444, V.1447, V.1448 Ligands: 6OU.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.406, A:F.1444, A:V.1447, A:V.1448 Hydrogen bonds: A:S.1394, A:S.1394

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

6OU.14: 8 residues within 4Å: Chain A: G.717, S.719, L.720, L.723, L.727, I.731 Ligands: Y01.28, Y01.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.727, A:L.727 Hydrogen bonds: A:S.719 6OU.15: 23 residues within 4Å: Chain A: A.954, W.955, L.958, S.985, T.988, L.989, L.992, L.995, L.998, V.1008, L.1011, V.1012, L.1347, V.1351, I.1354, Y.1355, F.1358, N.1362, V.1431, L.1434, F.1435, T.1438, I.1442 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.954, A:L.989, A:L.992, A:L.992, A:L.995, A:V.1008, A:L.1011, A:Y.1355, A:F.1358, A:L.1434, A:I.1442 Hydrogen bonds: A:N.1362 6OU.16: 26 residues within 4Å: Chain A: L.1022, C.1025, L.1026, W.1029, D.1087, N.1088, G.1090, A.1091, Y.1093, L.1094, L.1097, T.1101, L.1146, F.1149, P.1429, A.1430, I.1433, L.1434, T.1437, T.1438, I.1440, I.1441, F.1444 Ligands: XHO.13, Y01.21, Y01.23 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.1022, A:W.1029, A:Y.1093, A:L.1097, A:T.1101, A:F.1149, A:F.1149, A:A.1430, A:L.1434, A:I.1441 Hydrogen bonds: A:N.1088 6OU.17: 17 residues within 4Å: Chain A: V.256, V.259, F.260, F.359, A.360, F.363, M.1219, F.1220, C.1223, M.1226, M.1230, L.1320, A.1324, K.1325 Ligands: Y01.26, Y01.27, Y01.28 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.359, A:F.363, A:F.363 6OU.18: 21 residues within 4Å: Chain A: L.900, S.903, G.904, A.907, F.908, D.910, Y.912, R.916, P.994, A.997, F.1001, M.1004, L.1346, F.1349, L.1350, F.1353, T.1380, F.1381, A.1382, M.1385 Ligands: Y01.24 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.908, A:F.908, A:F.908, A:F.1349 Hydrogen bonds: A:L.900 6OU.19: 14 residues within 4Å: Chain A: L.400, G.1186, S.1274, W.1275, F.1278, L.1318, I.1321, R.1328, T.1329, L.1331, F.1332, L.1334, M.1335, L.1338 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1275, A:F.1278, A:L.1331, A:L.1334 Hydrogen bonds: A:S.1274 Salt bridges: A:R.1328

13 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.20: 11 residues within 4Å: Chain A: V.532, T.535, L.536, L.622, S.625, W.626, P.627, N.1020, L.1023, I.1027 Ligands: Y01.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.532, A:V.532, A:L.536, A:I.1027 Y01.21: 16 residues within 4Å: Chain A: L.536, A.539, L.540, H.542, Y.543, N.544, L.1026, I.1027, L.1030, N.1088, V.1089, G.1090, Y.1093 Ligands: 6OU.16, Y01.20, Y01.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.540, A:N.1088, A:V.1089 Hydrogen bonds: A:Y.1093 Y01.22: 5 residues within 4Å: Chain A: F.951, T.952, A.954, W.957, L.961 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.957, A:W.957, A:W.957 Y01.23: 7 residues within 4Å: Chain A: M.1019, L.1022, L.1026, G.1090, Y.1093 Ligands: 6OU.16, Y01.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1026 Y01.24: 12 residues within 4Å: Chain A: S.331, D.332, K.388, I.389, M.391, I.392, M.395, F.1349, A.1382, M.1385, L.1386 Ligands: 6OU.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.388, A:K.388, A:I.392, A:A.1382 Y01.25: 11 residues within 4Å: Chain A: L.1224, V.1227, T.1228, V.1231, E.1239, K.1240, I.1243, L.1244, I.1247, F.1251 Ligands: Y01.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1224, A:E.1239, A:K.1240, A:I.1243, A:L.1244, A:I.1247 Y01.26: 9 residues within 4Å: Chain A: F.359, A.360, V.1227, M.1230, V.1231, T.1233, K.1240 Ligands: 6OU.17, Y01.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.1230, A:V.1231 Y01.27: 16 residues within 4Å: Chain A: T.258, V.259, L.262, A.360, W.361, F.363, L.364, F.367, M.709, M.713, Q.718, L.722, L.726, V.730 Ligands: 6OU.17, Y01.28 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.361, A:W.361, A:F.363, A:L.364, A:L.364, A:L.364, A:F.367, A:L.722, A:L.722 Y01.28: 10 residues within 4Å: Chain A: Q.718, S.719, L.722, L.723, L.726, L.727, V.730 Ligands: 6OU.14, 6OU.17, Y01.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.718, A:L.722, A:L.723, A:V.730 Y01.29: 12 residues within 4Å: Chain A: F.265, I.268, L.272, S.330, S.331, I.389, Y.390, I.392, F.393, L.396, T.1304, L.1311 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.268, A:I.389, A:I.389, A:Y.390, A:F.393, A:T.1304 Y01.30: 18 residues within 4Å: Chain A: A.218, L.219, T.221, F.222, V.224, L.225, L.228, I.653, I.656, F.657, V.660, L.664, L.720, L.723, V.724, L.727, I.731 Ligands: 6OU.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.218, A:T.221, A:F.222, A:F.222, A:L.225, A:L.228, A:I.653, A:I.656, A:F.657, A:L.664, A:L.720, A:L.720, A:L.727 Y01.31: 13 residues within 4Å: Chain A: S.639, V.640, T.647, F.690, F.691, F.694, Y.1129, I.1132, V.1135, V.1136, I.1139, F.1140, F.1144 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.640, A:T.647, A:F.691, A:F.694, A:F.694, A:I.1132, A:I.1132, A:I.1139 Hydrogen bonds: A:Y.1129 Y01.32: 16 residues within 4Å: Chain A: V.610, S.613, L.617, F.620, F.1028, I.1031, F.1032, M.1035, L.1039, N.1127, Y.1129, M.1130, I.1132, Y.1133, V.1136, F.1140 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.610, A:F.1032, A:F.1032, A:Y.1133, A:F.1140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lenaeus, M. et al., Structural basis for inhibition of the cardiac sodium channel by the atypical antiarrhythmic drug ranolazine. Nat Cardiovasc Res (2023)

Release Date

2023-04-12

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