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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.540, A:N.1088, A:V.1089 Hydrogen bonds: A:Y.1093, 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 8 PLIP interactions: 8 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 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.J. et al., Structural Basis for Inhibition of the Cardiac Sodium Channel by the Atypical Antiarrhythmic Drug Ranolazine. To Be Published

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