SMTL ID : 8e5a.1

Human L-type voltage-gated calcium channel Cav1.3 treated with 1.4 mM 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: R.114, N.120, N.184 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: 2 residues within 4Å: Chain B: R.84, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: E.567, N.568, L.591, 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: 9 residues within 4Å: Chain B: Q.108, W.113, E.115, E.182, N.468, T.470, K.480, N.481, L.485 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.115

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.364, E.705, E.1101, G.1405, E.1406 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.364, A:E.705, A:E.1101, A:E.1101 CA.9: 5 residues within 4Å: Chain A: D.153 Chain B: D.259, S.261, S.263, T.331 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.261, B:S.263, B:T.331

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

NAG.7: 2 residues within 4Å: Chain B: K.88, N.92 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain B: F.780, N.781, K.782, R.873 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.782, B:K.782

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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