SMTL ID : 6jp5.1

Rabbit Cav1.1-Nifedipine Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-2-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG-NAG.1: 2 residues within 4Å: Chain C: N.348, N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: E.82, A.85, R.86, N.615 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.897, F.984 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain C: N.677 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: L.49, T.52, Q.725, I.728 Ligands: NAG.30 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 4 residues within 4Å: Chain C: R.116, N.122, N.186, W.187 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 12 residues within 4Å: Chain C: Q.110, W.115, E.117, E.184, W.187, N.470, T.472, T.479, L.481, K.482, N.483, L.487 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:T.479 Hydrogen bonds: C:K.482

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

NAG.8: 1 residues within 4Å: Chain A: N.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.257 NAG.23: 1 residues within 4Å: Chain C: N.326 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.326 NAG.24: 1 residues within 4Å: Chain C: N.890 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.890 NAG.25: 2 residues within 4Å: Chain C: L.91, N.94 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.91 Hydrogen bonds: C:N.94 NAG.26: 2 residues within 4Å: Chain C: R.591, N.606 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.591, C:R.591 NAG.27: 3 residues within 4Å: Chain C: F.782, N.783, R.875 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.875 NAG.28: 1 residues within 4Å: Chain C: N.1000 No protein-ligand interaction detected (PLIP) NAG.29: 3 residues within 4Å: Chain C: N.987, S.989, F.992 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.989 NAG.30: 4 residues within 4Å: Chain C: D.45, L.49, N.826 Ligands: NAG-NAG.7 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.49 Hydrogen bonds: C:N.826

3 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322, E.1323 Ligands: CA.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.292, A:E.1014, A:E.1014 CA.10: 3 residues within 4Å: Chain A: E.292, E.1014 Ligands: CA.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.292 CA.21: 4 residues within 4Å: Chain A: D.78 Chain C: S.263, S.265, T.333 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:S.263, C:S.265, C:T.333, A:D.78

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

3PE.11: 14 residues within 4Å: Chain A: P.1181, W.1182, F.1185, I.1244, R.1254, L.1257, W.1258, I.1261 Chain B: L.200, L.204, P.208, E.213, S.214, C.215 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:P.1181, A:W.1182, A:I.1244, A:R.1254, A:L.1257, A:L.1257, A:I.1261, B:L.200, B:L.204 Salt bridges: A:R.1254 Hydrogen bonds: B:E.213, B:C.215 3PE.12: 12 residues within 4Å: Chain A: I.208, N.277, F.278, G.279, M.282, M.1129, T.1132, G.1136, M.1137, Q.1138, H.1139 Ligands: 3PE.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.208, A:T.1132 Hydrogen bonds: A:N.277 Salt bridges: A:H.1139 3PE.13: 10 residues within 4Å: Chain A: Q.939, L.1001, S.1002, M.1005, F.1008, Y.1358, Y.1359, I.1362, M.1366 Ligands: C5U.18 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:M.1005, A:F.1008, A:Y.1359, A:I.1362, A:I.1362 3PE.14: 8 residues within 4Å: Chain A: N.277, G.279, P.630, Y.632, V.635, C.638, I.642 Ligands: 3PE.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.635 3PE.15: 10 residues within 4Å: Chain A: A.163, A.166, L.580, Y.627, G.628, P.633, G.634, L.636, I.639, Y.640 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.163, A:A.166, A:L.580, A:Y.627, A:P.633, A:I.639, A:Y.640 Hydrogen bonds: A:G.628 3PE.16: 8 residues within 4Å: Chain A: C.65, A.69, V.70, L.82, F.567, P.601, L.604 Ligands: 3PE.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.69, A:F.567, A:P.601, A:L.604 3PE.17: 8 residues within 4Å: Chain A: I.570, P.601, L.604, F.608, V.1039, E.1040, I.1046 Ligands: 3PE.16 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.570, A:L.604, A:L.604, A:F.608, A:I.1046 3PE.20: 8 residues within 4Å: Chain A: L.522, V.526, C.529, L.533, L.949, R.1038, M.1041, F.1044 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.533, A:F.1044, A:F.1044 Salt bridges: A:R.1038

1 x C5U: dimethyl 2,6-dimethyl-4-(2-nitrophenyl)-1,4-dihydropyridine-3,5-dicarboxylate(Non-covalent)

C5U.18: 12 residues within 4Å: Chain A: V.932, T.935, T.936, Q.939, F.1008, S.1011, Y.1048, I.1052, M.1057, M.1366, A.1369 Ligands: 3PE.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.932, A:I.1052 Hydrogen bonds: A:S.1011, A:S.1011

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

PC1.19: 13 residues within 4Å: Chain A: Y.210, L.217, F.218, K.221, A.304, I.305, W.309, P.310, I.312, Y.313, L.1237, M.1241 Chain B: F.152 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.217, A:F.218, A:W.309, A:I.312, A:Y.313, A:L.1237

1 x ETA: ETHANOLAMINE(Covalent)

ETA.22: 3 residues within 4Å: Chain C: Q.402, Y.412, C.1073 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.1073

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Molecular Basis for Ligand Modulation of a Mammalian Voltage-Gated Ca2+Channel. Cell (2019)

Release Date

2019-06-12

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
Voltage-dependent L-type calcium channel subunit beta-1: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
F

D
B

E
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

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

Voltage-dependent L-type calcium channel subunit beta-1

Related Entries With Identical Sequence