SMTL ID : 7jpk.1

Rabbit Cav1.1 in the presence of 100 micromolar (S)-(-)-Bay K8644 in nanodiscs at 3.0 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: 4 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.614, A:E.1014, A:E.1014

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

3PE.2: 12 residues within 4Å: Chain A: A.200, L.201, F.205, I.208, N.277, F.278, M.1129, T.1132, I.1133, G.1136, H.1139 Ligands: 3PE.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.200, A:L.201, A:F.205, A:I.208, A:F.278, A:T.1132, A:I.1133 Salt bridges: A:H.1139 3PE.3: 14 residues within 4Å: Chain A: L.933, T.936, L.1001, S.1002, M.1005, F.1060, Y.1358, Y.1359, I.1362, S.1363, M.1366, L.1367, F.1370 Ligands: C8U.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1060, A:Y.1359, A:I.1362, A:L.1367 3PE.4: 19 residues within 4Å: Chain A: A.200, V.203, N.277, G.279, F.280, M.282, L.283, Y.286, S.631, Y.632, V.635, L.636, C.638, I.639, I.642, I.643, V.646, C.647 Ligands: 3PE.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.200, A:V.203, A:Y.286, A:Y.286, A:L.636, A:I.639, A:I.642, A:I.643, A:V.646 Hydrogen bonds: A:N.277 3PE.5: 10 residues within 4Å: Chain A: A.163, A.166, L.170, F.573, L.576, L.580, R.584, Y.627, P.633, L.636 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.163, A:L.170, A:F.573, A:L.580, A:Y.627, A:P.633, A:L.636 Hydrogen bonds: A:Y.627 Salt bridges: A:R.584 3PE.6: 10 residues within 4Å: Chain A: F.62, C.65, A.69, V.70, F.567, I.571, F.600, L.604, I.1047 Ligands: 3PE.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.62, A:F.62, A:A.69, A:F.567, A:I.571, A:F.600, A:L.604, A:I.1047 3PE.7: 8 residues within 4Å: Chain A: F.567, P.601, V.1039, E.1040, A.1042, I.1043, I.1046 Ligands: 3PE.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.567, A:A.1042, A:I.1046, A:I.1046 3PE.9: 11 residues within 4Å: Chain A: L.522, V.526, C.529, L.533, M.941, F.942, I.945, E.1040, M.1041, F.1044, I.1047 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.533, A:F.942, A:F.942, A:I.945, A:F.1044 Hydrogen bonds: A:E.1040, A:E.1040 3PE.10: 16 residues within 4Å: Chain A: N.307, E.308, W.311, V.315, L.319, F.323, I.1274, V.1275, F.1278, T.1308, F.1309, P.1310, Q.1311, V.1313, L.1314, F.1317 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:W.311, A:W.311, A:W.311, A:W.311, A:V.315, A:L.319, A:F.323, A:I.1274, A:V.1275, A:V.1275, A:F.1278, A:F.1309, A:P.1310, A:P.1310, A:V.1313, A:L.1314, A:F.1317 Hydrogen bonds: A:Q.1311 3PE.12: 14 residues within 4Å: Chain A: P.1181, W.1182, R.1254, L.1257, W.1258, I.1261 Chain B: L.204, M.207, P.208, N.210, P.211, E.213, S.214, C.215 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.1181, A:W.1182, A:W.1182, A:L.1257, A:L.1257, A:W.1258, A:I.1261, B:L.204 Hydrogen bonds: A:R.1254, B:E.213, B:C.215

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

PC1.8: 16 residues within 4Å: Chain A: M.206, I.209, Y.210, I.213, L.217, F.218, K.221, I.305, W.309, I.312, Y.313, T.316, L.320, A.1233, F.1234, L.1237 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.209, A:L.217, A:W.309, A:I.312, A:T.316, A:L.320, A:F.1234, A:L.1237 Salt bridges: A:K.221

1 x C8U: methyl (4~{S})-2,6-dimethyl-5-nitro-4-[2-(trifluoromethyl)phenyl]-1,4-dihydropyridine-3-carboxylate(Non-covalent)

C8U.11: 13 residues within 4Å: Chain A: V.932, T.935, T.936, Q.939, F.1008, S.1011, T.1012, Y.1048, M.1056, M.1057, F.1060, M.1366 Ligands: 3PE.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.1012 Hydrogen bonds: 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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