SMTL ID : 7fbs.1

structure of a channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 6 residues within 4Å: Chain A: N.1072, G.1075, L.1077, Y.1078, W.1079 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1072 NAG.2: 4 residues within 4Å: Chain A: P.1409, P.1414, N.1415 Ligands: NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.1409 Hydrogen bonds: A:N.1415 NAG.3: 3 residues within 4Å: Chain A: N.284, E.338, R.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.284, A:E.338

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

6OU.4: 8 residues within 4Å: Chain A: A.360, W.361, F.363, F.367, Q.718, L.722, L.726 Ligands: 6OU.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.361, A:F.363, A:F.363, A:F.367, A:L.722, A:L.726 Hydrogen bonds: A:Q.718, A:Q.718 6OU.5: 4 residues within 4Å: Chain A: G.717, S.719, L.720, L.723 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.723 Hydrogen bonds: A:S.719 6OU.6: 3 residues within 4Å: Chain A: Q.718, L.722 Ligands: 6OU.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.722 6OU.7: 3 residues within 4Å: Chain A: V.1227, V.1231, T.1233 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1227, A:V.1231 6OU.8: 8 residues within 4Å: Chain A: N.1088, G.1090, Y.1093, A.1430, I.1433, L.1434, T.1437, T.1438 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1093, A:I.1433, A:L.1434 6OU.9: 12 residues within 4Å: Chain A: S.985, T.988, L.989, L.992, L.995, V.1008, V.1351, Y.1355, F.1358, N.1362, V.1431, L.1434 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.989, A:L.992, A:L.995, A:V.1008, A:V.1351, A:Y.1355, A:F.1358, A:F.1358 6OU.10: 4 residues within 4Å: Chain A: L.900, S.903, A.907, F.908 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.900, A:A.907, A:F.908 6OU.11: 6 residues within 4Å: Chain A: A.150, Q.151, H.152, D.689, F.690, Y.1129 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.150, A:F.690 Hydrogen bonds: A:F.690, A:Y.1129 Salt bridges: A:H.152 6OU.12: 3 residues within 4Å: Chain A: G.637, F.1140 Ligands: 6OU.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1140, A:F.1140 6OU.13: 5 residues within 4Å: Chain A: W.585, L.617, F.620, M.1035 Ligands: 6OU.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.585, A:L.617 6OU.15: 16 residues within 4Å: Chain A: I.409, L.410, L.650, F.698, L.701, C.702, G.703, N.733, V.736, L.737, F.740, F.1102, F.1143, L.1146 Ligands: 4Y4.14, 9Z9.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.409, A:L.410, A:L.650, A:F.698, A:V.736, A:L.737, A:F.1143 Hydrogen bonds: A:N.733

1 x 4Y4: 1-[2-[(2R)-2-oxidanyl-3-(propylamino)propoxy]phenyl]-3-phenyl-propan-1-one(Non-covalent)

4Y4.14: 11 residues within 4Å: Chain A: Q.372, F.403, N.407, T.1392, T.1393, F.1444, V.1448, Y.1451, I.1452 Ligands: 6OU.15, 9Z9.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.403, A:F.1444, A:Y.1451, A:Y.1451, A:I.1452

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

9Z9.16: 8 residues within 4Å: Chain A: L.410, A.414, E.418, F.740, L.741, I.1455 Ligands: 4Y4.14, 6OU.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.410, A:A.414, A:F.740, A:L.741, A:I.1455 Hydrogen bonds: A:E.418 9Z9.17: 11 residues within 4Å: Chain A: F.403, Y.404, N.407, L.408, A.1333, L.1341, Y.1451, I.1454, I.1455, N.1458, F.1459 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.403, A:Y.404, A:L.408, A:A.1333, A:L.1341, A:Y.1451, A:Y.1451, A:I.1454, A:I.1455, A:F.1459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, D. et al., Open-state structure and pore gating mechanism of the cardiac sodium channel. Cell (2021)

Release Date

2021-09-22

Peptides

Sodium channel protein type 5 subunit alpha,Sodium channel protein type 5 subunit alpha,Sodium channel protein type 5 subunit alpha,G protein/GFP fusion 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,Sodium channel protein type 5 subunit alpha,Sodium channel protein type 5 subunit alpha,G protein/GFP fusion protein