SMTL ID : 7jpx.1

Rabbit Cav1.1 in the presence of 100 micromolar amlodipine in nanodiscs at 2.9 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322, E.1323 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.292, A:E.614, A:E.1014, A:E.1014

9 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)

3PE.2: 11 residues within 4Å: Chain A: P.1181, W.1182, L.1247, R.1254, W.1258 Chain B: L.204, M.207, P.208, P.211, E.213, C.215 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.204, A:P.1181, A:W.1182, A:R.1254 Hydrogen bonds: B:E.213, B:C.215, A:R.1254 3PE.3: 13 residues within 4Å: Chain A: A.200, L.204, F.205, I.208, N.277, F.278, G.279, M.282, M.1129, T.1132, G.1136, H.1139 Ligands: 3PE.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.200, A:L.204, A:F.205, A:F.205, A:I.208, A:F.278, A:T.1132 Hydrogen bonds: A:N.277, A:G.279, A:H.1139 Salt bridges: A:H.1139 3PE.4: 16 residues within 4Å: Chain A: I.928, V.932, L.933, T.936, L.937, L.1001, S.1002, M.1005, F.1008, F.1060, Y.1358, Y.1359, M.1366, L.1367, F.1370 Ligands: 6UB.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.928, A:V.932, A:L.933, A:T.936, A:L.937, A:F.1008, A:F.1060, A:Y.1358, A:Y.1359, A:Y.1359, A:M.1366, A:L.1367, A:L.1367, A:F.1370, A:F.1370 3PE.5: 14 residues within 4Å: Chain A: G.279, F.280, L.283, P.630, S.631, Y.632, V.635, L.636, C.638, I.642, V.646, C.647 Ligands: 3PE.3, POV.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.283, A:Y.632, A:I.642, A:I.642, A:V.646 Hydrogen bonds: A:N.277, A:Y.632 3PE.6: 10 residues within 4Å: Chain A: A.163, A.166, F.573, L.576, R.584, Y.627, P.633, L.636, I.639, I.643 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.163, A:A.166, A:F.573, A:F.573, A:L.576, A:Y.627, A:P.633, A:I.643 Hydrogen bonds: A:Y.627 Salt bridges: A:R.584 3PE.7: 13 residues within 4Å: Chain A: F.62, C.65, A.69, V.70, L.175, F.567, I.571, N.599, F.600, P.601, L.604, I.1047 Ligands: 3PE.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.62, A:L.175, A:F.567, A:L.604, A:I.1047 3PE.8: 9 residues within 4Å: Chain A: F.567, I.570, P.601, L.604, F.608, V.1039, E.1040, I.1046 Ligands: 3PE.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.567, A:I.570, A:L.604, A:F.608, A:I.1046, A:I.1046 Hydrogen bonds: A:E.1040 3PE.10: 7 residues within 4Å: Chain A: L.522, C.529, F.942, I.945, E.1040, M.1041, F.1044 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.942, A:F.942, A:I.945, A:F.1044 Hydrogen bonds: A:E.1040, A:E.1040 3PE.11: 12 residues within 4Å: Chain A: N.307, E.308, W.311, V.315, F.323, V.1275, F.1278, T.1308, P.1310, Q.1311, L.1314, F.1317 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.311, A:V.315, A:F.323, A:F.323, A:V.1275, A:F.1278, A:P.1310, A:L.1314, A:F.1317 Hydrogen bonds: A:T.1308

1 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.9: 17 residues within 4Å: Chain A: Y.210, I.213, L.217, F.218, I.305, W.309, P.310, I.312, Y.313, T.316, L.320, A.1233, F.1234, L.1237, M.1241, I.1244 Chain B: Q.160 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.210, A:L.217, A:W.309, A:I.312, A:Y.313, A:Y.313, A:T.316, A:L.320, A:F.1234, A:L.1237, A:I.1244

1 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.12: 13 residues within 4Å: Chain A: V.203, I.289, T.290, M.291, G.321, L.326, F.645, N.649, Y.650, M.1057, Y.1365 Ligands: 3PE.5, 6UB.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.203, A:L.326, A:L.326, A:N.649

1 x 6UB: amlodipine(Non-covalent)

6UB.13: 16 residues within 4Å: Chain A: V.932, T.935, T.936, Q.939, F.1008, S.1011, T.1012, Y.1048, I.1052, M.1056, M.1057, F.1060, M.1366, I.1373 Ligands: 3PE.4, POV.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Q.939, A:F.1060, A:F.1060, A:I.1373 Hydrogen bonds: A:S.1011, A:S.1011, A:S.1011

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, S. et al., Structural Basis of the Modulation of the Voltage-Gated Calcium Ion Channel Ca v 1.1 by Dihydropyridine Compounds*. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2020-11-18

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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