SMTL ID : 8we8.1

Human L-type voltage-gated calcium channel Cav1.2 in the presence of calciseptine, amlodipine and pinaverium at 2.9 Angstrom resolution

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-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: 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: 4 residues within 4Å: Chain B: E.80, A.83, R.84, 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, L.479, K.480, N.481, L.485 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.115, B:E.115

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.363, E.706, E.1115, G.1443 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.363, A:E.363, A:E.706, A:E.1115 CA.15: 4 residues within 4Å: Chain A: D.151 Chain B: S.261, S.263, T.331 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.151, B:S.261, B:S.263

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 6 residues within 4Å: Chain A: I.915, A.918, R.929, V.1396, T.1429, F.1430 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.915, A:A.918, A:V.1396, A:T.1429, A:F.1430, A:F.1430 CLR.8: 11 residues within 4Å: Chain A: F.665, L.668, L.672, Y.719, P.725, L.728, V.729, I.731, Y.732, I.735 Ligands: CLR.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.665, A:F.665, A:L.668, A:L.672, A:Y.719, A:Y.719, A:P.725, A:V.729, A:V.729, A:I.731, A:Y.732, A:I.735 CLR.9: 5 residues within 4Å: Chain A: N.348, I.1234, A.1237, M.1238, H.1240 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1234, A:A.1237, A:M.1238, A:H.1240 CLR.10: 9 residues within 4Å: Chain A: F.231, D.232, A.235, A.238, F.239, V.241, L.242, L.668 Ligands: CLR.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.232, A:A.235, A:A.238, A:F.239, A:V.241, A:L.242, A:L.242 Hydrogen bonds: A:D.232 CLR.18: 8 residues within 4Å: Chain A: F.535, T.538, L.539, H.545, N.1100, L.1102 Chain D: T.43, M.45 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.535, A:T.538, A:L.1102 Hydrogen bonds: D:T.43, D:T.43

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

NAG.11: 1 residues within 4Å: Chain A: N.1416 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: K.88, N.92, E.199, D.200 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.199 Hydrogen bonds: B:D.200 NAG.17: 2 residues within 4Å: Chain B: N.781, R.873 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.781, B:R.873

1 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate(Non-covalent)

PT5.12: 13 residues within 4Å: Chain A: V.278, Y.282, I.285, P.1282, W.1283, F.1286, M.1362, E.1372, R.1375, T.1376, L.1378, W.1379, D.1523 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.278, A:I.285, A:P.1282, A:W.1283, A:F.1286, A:F.1286 Hydrogen bonds: A:R.1375, A:T.1376, A:T.1376, A:D.1523

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

3PE.13: 10 residues within 4Å: Chain A: H.322, R.378, D.379, W.382, V.386, F.1399, P.1431, V.1434, L.1435, F.1438 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.382, A:W.382, A:W.382, A:W.382, A:V.386, A:F.1399, A:P.1431, A:P.1431, A:L.1435, A:F.1438 Hydrogen bonds: A:H.322, A:R.378, A:Q.1432

1 x 6UB: amlodipine(Non-covalent)

6UB.14: 11 residues within 4Å: Chain A: V.1033, T.1036, T.1037, Q.1040, F.1109, S.1112, T.1113, Y.1149, I.1153, A.1154, M.1489 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1033, A:T.1036, A:I.1153 Hydrogen bonds: A:S.1112, A:S.1112, A:A.1154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Structural basis for human Ca v 1.2 inhibition by multiple drugs and the neurotoxin calciseptine. Cell (2023)

Release Date

2023-12-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent L-type calcium channel subunit alpha-1C

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

Voltage-dependent L-type calcium channel subunit beta-3

Calciseptin

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