SMTL ID : 8e59.1

Human L-type voltage-gated calcium channel Cav1.3 in the presence of Amiodarone at 3.1 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: 4 residues within 4Å: Chain B: R.114, 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: 2 residues within 4Å: Chain B: N.346, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: A.83, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: E.567, N.568, L.591, 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, T.477, K.480, N.481, L.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.115, B:E.115

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

BBI.6: 12 residues within 4Å: Chain A: I.1012, M.1019, T.1022, S.1098, F.1100, A.1140, M.1144, F.1147, Y.1448, L.1450, A.1452, F.1453 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1012, A:M.1019, A:F.1100, A:A.1140, A:M.1144, A:L.1450, A:A.1452, A:F.1453

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: E.364, E.705, E.1101, G.1405 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.364, A:E.364, A:E.705, A:E.1101, A:E.1101 CA.11: 5 residues within 4Å: Chain A: D.153 Chain B: D.259, S.261, S.263, T.331 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Metal complexes: A:D.153, B:S.261, B:S.263, B:T.331

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

3PE.8: 11 residues within 4Å: Chain A: F.658, I.661, P.692, L.695, L.696, F.699, V.1126, E.1127, S.1129, I.1133, I.1137 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.658, A:I.661, A:L.695, A:L.695, A:L.696, A:L.696, A:F.699, A:I.1133, A:I.1133, A:I.1137 Hydrogen bonds: A:S.1129

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

NAG.9: 2 residues within 4Å: Chain B: K.88, N.92 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.88, B:K.88 NAG.10: 3 residues within 4Å: Chain B: F.780, N.781, K.782 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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