SMTL ID : 7uhf.1

Human L-type voltage-gated calcium channel Cav1.3 in the presence of cinnarizine 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: 1 residues within 4Å: Chain B: N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: T.610, P.611, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain B: E.567, N.568, L.591, 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 N90: 1-(diphenylmethyl)-4-[(2E)-3-phenylprop-2-en-1-yl]piperazine(Non-covalent)

N90.6: 11 residues within 4Å: Chain A: F.699, L.702, T.703, N.740, L.743, L.744, F.747, F.1100, A.1140, M.1144, T.1404 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.699, A:T.703, A:L.743, A:L.743, A:L.744, A:F.747, A:F.747, A:A.1140 Hydrogen bonds: A:N.740

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

NAG.7: 1 residues within 4Å: Chain A: N.329 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.329 NAG.11: 2 residues within 4Å: Chain B: N.92, E.199 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.199 NAG.12: 2 residues within 4Å: Chain B: N.781, K.782 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.13: 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 Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 5 residues within 4Å: Chain A: L.538, S.541, S.542, H.544, N.1086 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:H.544, A:N.1086

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

3PE.10: 11 residues within 4Å: Chain A: W.383, A.1358, F.1361, F.1362, T.1391, F.1392, P.1393, Q.1394, V.1396, L.1397, F.1400 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.383, A:W.383, A:F.1361, A:F.1361, A:F.1392, A:P.1393, A:P.1393, A:F.1400 Hydrogen bonds: A:T.1391, A:Q.1394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, X. et al., Structural basis for pore blockade of human voltage-gated calcium channel Ca v 1.3 by motion sickness drug cinnarizine. Cell Res. (2022)

Release Date

2022-05-11

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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