SMTL ID : 8e5b.1

Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone and Sofosbuvir at 3.3 Angstrom resolution

Coordinates

PDB Format Compare

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: E.80, A.83, R.84, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: E.567, A.893, F.894, N.895, F.982 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.115

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

BBI.6: 15 residues within 4Å: Chain A: M.1019, T.1022, T.1023, F.1095, S.1098, T.1099, F.1100, A.1140, M.1144, F.1147, Y.1448, M.1449, L.1450, F.1453 Ligands: WG6.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.1019, A:T.1022, A:F.1100, A:L.1450, A:F.1453, A:F.1453

1 x WG6: Sofosbuvir(Non-covalent)

WG6.7: 9 residues within 4Å: Chain A: M.363, L.398, N.740, L.744, N.1145, A.1403, Y.1448, I.1455 Ligands: BBI.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.744, A:I.1455 Hydrogen bonds: A:N.740

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 3 residues within 4Å: Chain A: E.364, E.1101, G.1405 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.364, A:E.1101 CA.10: 4 residues within 4Å: Chain A: D.153 Chain B: S.261, S.263, T.331 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Metal complexes: B:S.261, B:S.263, B:T.331, A:D.153

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

NAG.9: 3 residues within 4Å: Chain B: K.88, N.92, E.199 No protein-ligand interaction detected (PLIP)

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-1D: 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-1D

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

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

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