SMTL ID : 7uhg.1

Human L-type voltage-gated calcium channel Cav1.3 at 3.0 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)

NAG-NAG.1: 1 residues within 4Å: Chain B: N.329 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.346, N.348 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: E.80, A.83, R.84, N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: N.568, L.591, A.893, F.894, N.895 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.2: 4 residues within 4Å: Chain C: R.114, N.120, N.184, W.185 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.4: 9 residues within 4Å: Chain C: Q.108, W.113, E.115, N.468, T.470, T.477, K.480, N.481, L.485 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.115

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain B: E.364, E.705, E.1101, G.1405, E.1406 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.364, B:E.364, B:E.705, B:E.1101, B:E.1101 CA.14: 4 residues within 4Å: Chain B: D.153 Chain C: S.261, S.263, T.331 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Metal complexes: B:D.153, C:S.261, C:S.263, C:T.331

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.8: 8 residues within 4Å: Chain B: F.534, L.538, S.541, S.542, H.544, F.1027, N.1086, L.1088 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.534, B:L.538, B:L.538, B:F.1027, B:N.1086 CLR.9: 5 residues within 4Å: Chain B: L.898, A.902, I.918, L.919, F.922 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.898, B:A.902, B:I.918, B:L.919, B:F.922 CLR.11: 6 residues within 4Å: Chain B: L.1025, F.1029, E.1127, I.1128, F.1131, I.1138 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.1025, B:F.1029, B:F.1029, B:F.1131, B:F.1131, B:I.1138 Hydrogen bonds: B:E.1127, B:E.1127

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

3PE.10: 11 residues within 4Å: Chain B: F.379, W.383, V.387, F.1361, R.1385, N.1388, P.1393, Q.1394, V.1396, L.1397, F.1400 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.383, B:W.383, B:W.383, B:V.387, B:F.1361, B:P.1393, B:P.1393, B:L.1397, B:F.1400 Hydrogen bonds: B:R.1385, B:N.1388, B:Q.1394

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

NAG.12: 3 residues within 4Å: Chain C: K.88, N.92, E.199 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain C: F.780, N.781, K.782, R.873 No protein-ligand interaction detected (PLIP)

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 beta-3: A
Voltage-dependent L-type calcium channel subunit alpha-1D: B
Voltage-dependent calcium channel subunit alpha-2/delta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
D

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent L-type calcium channel subunit beta-3

Voltage-dependent L-type calcium channel subunit alpha-1D

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

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