SMTL ID : 8e56.1

Rabbit L-type voltage-gated calcium channel Cav1.1 in the presence of Amiodarone at 2.8 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: 3 residues within 4Å: Chain C: L.593, N.898, 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: 10 residues within 4Å: Chain C: K.41, D.45, T.48, L.49, T.52, I.729, G.731, S.823, N.827, K.830 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: 10 residues within 4Å: Chain C: Q.110, W.115, E.117, E.184, N.470, T.472, T.479, K.482, N.483, L.487 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.482

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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: 15 residues within 4Å: Chain A: V.932, S.1011, T.1012, F.1013, A.1053, M.1057, F.1060, V.1061, Y.1365, M.1366, L.1367, A.1369, F.1370, I.1373 Ligands: 3PE.10 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.932, A:F.1013, A:M.1057, A:L.1367, A:A.1369, A:F.1370, A:I.1373

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

3PE.10: 15 residues within 4Å: Chain A: L.194, L.196, F.197, V.203, I.289, T.290, M.291, G.321, I.325, L.326, V.646, A.1320, T.1321, G.1322 Ligands: BBI.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.194, A:L.196, A:F.197, A:F.197, A:I.289, A:I.325, A:L.326, A:V.646, A:V.646 Hydrogen bonds: A:T.1321

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(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, N.94, E.201 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.90 Hydrogen bonds: C:K.90 NAG.15: 2 residues within 4Å: Chain C: R.591, N.606 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.591 NAG.16: 1 residues within 4Å: Chain C: N.784 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain C: N.1001, C.1002 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1001 NAG.18: 1 residues within 4Å: Chain C: N.988 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-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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