SMTL ID : 8fhs.1

Human L-type voltage-gated calcium channel Cav1.2 in the presence of amiodarone and sofosbuvir at 3.3 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 3 residues within 4Å: Chain B: N.120, N.184, W.185 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain B: N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: R.84, T.610, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: N.568, A.893, F.894, N.895, F.982, D.984 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG.3: 10 residues within 4Å: Chain B: Q.108, W.113, E.115, E.182, N.468, T.470, L.479, K.480, N.481, L.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.115, B:E.115

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.363, E.706, E.1135, G.1463, E.1464 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.363, A:E.706, A:E.1135 CA.15: 4 residues within 4Å: Chain A: D.151 Chain B: S.261, S.263, T.331 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.151, B:S.263, B:T.331

1 x BBI: (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone(Non-covalent)

BBI.7: 15 residues within 4Å: Chain A: I.1046, V.1053, T.1056, T.1057, S.1132, F.1134, A.1174, M.1178, F.1181, Y.1508, M.1509, L.1510, F.1513 Ligands: WG6.8, 3PE.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.1046, A:V.1053, A:T.1056, A:F.1134, A:F.1134, A:L.1510, A:F.1513

1 x WG6: Sofosbuvir(Non-covalent)

WG6.8: 13 residues within 4Å: Chain A: M.362, F.394, L.397, L.401, N.741, L.745, N.1179, V.1182, A.1461, A.1512, I.1515, I.1516 Ligands: BBI.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.394, A:L.397, A:L.401, A:L.745, A:V.1182, A:A.1512, A:I.1516 Hydrogen bonds: A:N.741

2 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.9: 11 residues within 4Å: Chain A: H.322, R.378, D.379, W.382, F.394, P.1451, Q.1452, V.1454, L.1455, F.1458 Ligands: CLR.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.382, A:W.382, A:F.394, A:P.1451, A:P.1451, A:V.1454, A:L.1455, A:F.1458 Hydrogen bonds: A:H.322, A:R.378 Salt bridges: A:R.378 3PE.11: 13 residues within 4Å: Chain A: Q.1060, L.1122, M.1125, M.1126, F.1129, M.1178, S.1498, V.1501, F.1502, I.1505, S.1506, M.1509 Ligands: BBI.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1122, A:V.1501, A:F.1502, A:I.1505, A:I.1505 Hydrogen bonds: A:S.1498

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 6 residues within 4Å: Chain A: I.915, A.918, A.919, R.929, F.1450 Ligands: 3PE.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.915, A:A.918, A:A.919, A:F.1450, A:F.1450 CLR.12: 7 residues within 4Å: Chain A: F.535, T.538, L.539, A.542, H.545, N.1120, L.1122 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.535, A:T.538, A:L.539, A:L.1122, A:L.1122 CLR.13: 9 residues within 4Å: Chain A: F.665, L.668, L.672, Y.719, P.725, L.728, V.729, I.731, I.735 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.668, A:Y.719, A:I.731, A:I.735, A:I.735 CLR.14: 8 residues within 4Å: Chain A: I.280, N.348, F.349, T.1253, I.1254, A.1257, M.1258, H.1260 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.280, A:F.349, A:F.349, A:F.349, A:T.1253, A:I.1254, A:I.1254, A:A.1257, A:H.1260

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

NAG.16: 3 residues within 4Å: Chain B: K.88, N.92, E.199 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.88, B:K.88 NAG.17: 3 residues within 4Å: Chain B: F.780, N.781, K.782 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.781, B:K.782

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Structural basis for human Ca v 1.2 inhibition by multiple drugs and the neurotoxin calciseptine. Cell (2023)

Release Date

2023-12-13

Peptides

Voltage-dependent L-type calcium channel subunit alpha-1C: A
Voltage-dependent calcium channel subunit alpha-2/delta-1: B
Voltage-dependent L-type calcium channel subunit beta-3: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent L-type calcium channel subunit alpha-1C

Voltage-dependent calcium channel subunit alpha-2/delta-1

Voltage-dependent L-type calcium channel subunit beta-3

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