SMTL ID : 8hmb.1

Cryo-EM structure of human high-voltage activated L-type calcium channel CaV1.2 in complex with benidipine (BEN)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

8 x R16: HEXADECANE(Non-covalent)

R16.1: 5 residues within 4Å: Chain B: Q.1040, M.1105, M.1106, F.1109 Ligands: 01.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.1106, B:F.1109 R16.2: 4 residues within 4Å: Chain B: T.538, L.539, H.545, L.1102 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.538, B:L.539, B:L.1102 R16.4: 3 residues within 4Å: Chain B: Y.282, T.1326 Ligands: R16.5 No protein-ligand interaction detected (PLIP) R16.5: 4 residues within 4Å: Chain B: Y.282, R.1347, L.1350 Ligands: R16.4 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.282, B:R.1347, B:L.1350 R16.6: 9 residues within 4Å: Chain B: N.348, A.350, F.351, P.722, S.723, F.724, M.727, L.728, I.731 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.350, B:F.351, B:L.728, B:I.731 R16.8: 8 residues within 4Å: Chain B: F.659, P.693, F.700, V.1140, E.1141, S.1143, I.1144, I.1147 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.659, B:P.693, B:F.700, B:I.1147 R16.9: 3 residues within 4Å: Chain B: V.139, N.158, L.159 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.139, B:L.159 R16.10: 4 residues within 4Å: Chain B: M.1238, H.1240, S.1244, F.1247 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.1247

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

3PE.3: 7 residues within 4Å: Chain B: R.378, W.382, F.1402, P.1403, Q.1404, V.1406, L.1407 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.382, B:W.382, B:F.1402, B:P.1403, B:P.1403, B:V.1406 3PE.7: 3 residues within 4Å: Chain B: D.232, A.235, F.239 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.232, B:A.235, B:F.239 3PE.12: 10 residues within 4Å: Chain B: L.268, V.275, I.360, M.362, S.393, V.396, L.397, I.738, N.741, Y.742 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.268, B:L.268, B:I.360, B:V.396, B:I.738, B:N.741

1 x 01: (3R)-1-benzylpiperidin-3-yl methyl (2R,3R,4R,5R,6S)-2,6-dimethyl-4-(3-nitrophenyl)piperidine-3,5-dicarboxylate

01.11: 16 residues within 4Å: Chain B: I.1026, I.1032, V.1033, T.1036, T.1037, Q.1040, F.1109, S.1112, I.1153, M.1157, M.1158, F.1161, M.1461, A.1464, F.1465 Ligands: R16.1 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.1026, B:T.1036, B:I.1153, B:M.1158, B:F.1161, B:A.1464, B:F.1465, B:F.1465 Hydrogen bonds: B:S.1112

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 3 residues within 4Å: Chain B: E.363, E.1115, G.1415 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.363 CA.14: 3 residues within 4Å: Chain B: E.363, E.706, E.1115 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.363, B:E.706, B:E.1115

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

NAG.15: 2 residues within 4Å: Chain C: K.88, N.92 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.92 NAG.16: 3 residues within 4Å: Chain C: R.114, N.120, N.184 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.114, C:N.120 NAG.17: 1 residues within 4Å: Chain C: N.324 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.324 NAG.18: 2 residues within 4Å: Chain C: F.780, N.781 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.780 Hydrogen bonds: C:N.781 NAG.19: 8 residues within 4Å: Chain C: Q.108, W.113, N.468, T.470, L.479, K.480, N.481, L.485 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.485 Hydrogen bonds: C:Q.108, C:N.468, C:N.481 NAG.20: 3 residues within 4Å: Chain C: E.80, P.611, N.613 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.80 Hydrogen bonds: C:N.613 NAG.21: 2 residues within 4Å: Chain C: N.346, N.348 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.348 NAG.22: 6 residues within 4Å: Chain C: L.566, E.567, A.893, F.894, N.895, D.984 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.566 Hydrogen bonds: C:N.895

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, Y. et al., Structural bases of inhibitory mechanism of Ca V 1.2 channel inhibitors. Nat Commun (2024)

Release Date

2024-04-24

Peptides

Isoform 2c of Voltage-dependent L-type calcium channel subunit beta-2: A
Voltage-dependent L-type calcium channel subunit alpha: B
Voltage-dependent calcium channel subunit alpha-2/delta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
E

Membrane

We predict this structure to be a membrane protein.
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Isoform 2c of Voltage-dependent L-type calcium channel subunit beta-2

Voltage-dependent L-type calcium channel subunit alpha

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

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