SMTL ID : 8e58.1

Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone and 1 mM MNI-1 at 3.0 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG-NAG.1: 1 residues within 4Å: Chain C: N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain C: E.82, N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: L.593, N.898, K.899, F.985 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.678, T.680, E.681 No protein-ligand interaction detected (PLIP)

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.5: 7 residues within 4Å: Chain C: D.45, L.49, T.52, I.729, G.731, S.823, N.827 No protein-ligand interaction detected (PLIP)

2 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.6: 4 residues within 4Å: Chain C: R.116, N.122, N.186, W.187 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 8 residues within 4Å: Chain C: Q.110, W.115, N.470, T.472, T.479, K.482, N.483, L.487 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.292, A:E.292, A:E.614, A:E.1014 CA.11: 4 residues within 4Å: Chain A: D.78 Chain C: S.263, S.265, T.333 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:S.263, C:S.265, C:T.333

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

BBI.9: 16 residues within 4Å: Chain A: I.925, V.932, T.935, T.936, S.1011, T.1012, F.1013, A.1053, M.1057, F.1060, Y.1365, M.1366, L.1367, A.1369, F.1370 Ligands: WFR.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.925, A:V.932, A:T.935, A:F.1060, A:L.1367, A:A.1369, A:F.1370 Halogen bonds: A:S.1011

1 x WFR: propan-2-yl (2S)-2-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-ethynyl-3-hydroxy-4-methyloxolan-2-yl]methoxy}(phenoxy)phosphoryl]amino}propanoate (non-preferred name)(Non-covalent)

WFR.10: 16 residues within 4Å: Chain A: M.291, S.322, F.323, L.326, L.330, N.649, L.653, F.1013, A.1053, F.1054, N.1058, V.1061, A.1369, I.1372, I.1373 Ligands: BBI.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.323, A:F.323, A:L.326, A:L.326, A:L.330, A:L.330, A:L.653, A:F.1013, A:F.1054, A:V.1061, A:I.1372 Hydrogen bonds: A:N.649, A:N.649

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

NAG.12: 1 residues within 4Å: Chain C: N.326 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain C: N.891 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain C: K.90, L.91, N.94 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.91 Hydrogen bonds: C:K.90, C:K.90, C:K.90, C:N.94 NAG.15: 2 residues within 4Å: Chain C: R.591, N.606 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain C: F.783, N.784, R.876 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.784 NAG.17: 2 residues within 4Å: Chain C: G.1000, N.1001 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.1000 NAG.18: 4 residues within 4Å: Chain C: I.892, S.893, N.988, S.990 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:N.988 Hydrogen bonds: C:I.892, C:S.990

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, X. et al., Structural basis for the severe adverse interaction of sofosbuvir and amiodarone on L-type Ca v channels. Cell (2022)

Release Date

2022-12-07

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
F

Membrane

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

Voltage-dependent calcium channel gamma-1 subunit

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

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