SMTL ID : 6uz0.1

Cardiac sodium channel with flecainide

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, S.1066 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1072, G.1075, L.1077, W.1079 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: 4 residues within 4Å: Chain A: H.279, N.329, R.341, K.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.341, A:R.341

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

NAG.4: 4 residues within 4Å: Chain A: N.319, R.384, W.1368, D.1374 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.1374 Hydrogen bonds: A:N.319 NAG.5: 2 residues within 4Å: Chain A: N.284, R.341 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.284

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

9Z9.6: 8 residues within 4Å: Chain A: D.332, K.388, I.389, M.391, M.395, A.1382, L.1386 Ligands: 6OU.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.388, A:I.389, A:A.1382, A:L.1386 9Z9.7: 3 residues within 4Å: Chain A: T.1228, I.1243, I.1247 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1243, A:I.1243 9Z9.8: 6 residues within 4Å: Chain A: A.539, L.540, H.542, N.1088 Ligands: 9Z9.9, 6OU.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.539, A:L.540, A:H.542 9Z9.9: 6 residues within 4Å: Chain A: V.532, L.536, L.1023, I.1027, L.1030 Ligands: 9Z9.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.536, A:L.1023, A:I.1027 9Z9.10: 8 residues within 4Å: Chain A: L.1039, N.1127, Y.1129, M.1130, I.1132, Y.1133, V.1136 Ligands: 6OU.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1039, A:I.1132, 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)(Non-functional Binders)

6OU.11: 5 residues within 4Å: Chain A: A.360, W.361, S.719, L.722 Ligands: 6OU.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.361, A:W.361, A:W.361 6OU.12: 4 residues within 4Å: Chain A: S.716, G.717, S.719 Ligands: 6OU.11 No protein-ligand interaction detected (PLIP) 6OU.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 6OU.14: 1 residues within 4Å: Chain A: V.1231 No protein-ligand interaction detected (PLIP) 6OU.15: 7 residues within 4Å: Chain A: G.1090, A.1091, L.1097, A.1430, I.1433, L.1434, I.1441 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1097, A:I.1433, A:L.1434, A:I.1441 6OU.16: 5 residues within 4Å: Chain A: S.985, T.988, L.989, L.995, F.1358 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.989, A:L.995 6OU.17: 2 residues within 4Å: Chain A: L.540 Ligands: 9Z9.8 No protein-ligand interaction detected (PLIP) 6OU.18: 5 residues within 4Å: Chain A: L.900, A.907, F.908, F.1001 Ligands: 9Z9.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.900, A:F.1001 6OU.19: 6 residues within 4Å: Chain A: A.150, Q.151, F.690, F.691, V.1136 Ligands: 6OU.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.150, A:V.1136 6OU.20: 3 residues within 4Å: Chain A: V.1136, F.1140 Ligands: 6OU.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1136, A:F.1140, A:F.1140 6OU.21: 4 residues within 4Å: Chain A: F.620, I.633, F.1140 Ligands: 9Z9.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.620, A:F.620, A:F.620, A:F.1140

1 x K4D: Flecainide(Non-covalent)

K4D.22: 13 residues within 4Å: Chain A: F.698, L.701, C.702, L.737, F.740, T.1101, F.1102, K.1103, I.1138, S.1142, F.1143, L.1146, S.1394 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1102, A:L.1146 Hydrogen bonds: A:K.1103

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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