SMTL ID : 6jpa.1

Rabbit Cav1.1-Verapamil Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

4 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 E: N.320, N.322 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain E: E.54, A.57, R.58, N.587 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain E: N.869, F.956 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain E: N.649 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 E: R.88, N.94, N.158, W.159 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 12 residues within 4Å: Chain E: Q.82, W.87, E.89, E.156, W.159, N.442, T.444, T.451, L.453, K.454, N.455, L.459 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:T.451 Hydrogen bonds: E:K.454

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.7: 6 residues within 4Å: Chain E: D.17, L.21, T.24, Q.697, I.700, N.798 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: N.257, G.258 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.257 NAG.26: 1 residues within 4Å: Chain E: N.298 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.298 NAG.27: 1 residues within 4Å: Chain E: N.862 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.862 NAG.28: 2 residues within 4Å: Chain E: L.63, N.66 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.63 Hydrogen bonds: E:N.66 NAG.29: 2 residues within 4Å: Chain E: R.563, N.578 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.563, E:R.563 NAG.30: 3 residues within 4Å: Chain E: F.754, N.755, R.847 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.847 NAG.31: 1 residues within 4Å: Chain E: N.972 No protein-ligand interaction detected (PLIP) NAG.32: 3 residues within 4Å: Chain E: N.959, S.961, F.964 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.961

3 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: E.292, E.614, E.1014, E.1323 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.292, A:E.292, A:E.1014 CA.10: 6 residues within 4Å: Chain A: E.292, T.612, G.613, E.614, F.1013 Ligands: 3PE.20 No protein-ligand interaction detected (PLIP) CA.24: 6 residues within 4Å: Chain A: D.78 Chain E: D.233, S.235, S.237, T.305, G.338 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Metal complexes: E:T.305, A:D.78

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

3PE.11: 13 residues within 4Å: Chain A: P.1181, W.1182, L.1247, R.1254, L.1257, W.1258, I.1261 Chain B: L.200, L.204, P.208, P.211, E.213, C.215 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.1182, A:L.1247, A:R.1254, A:L.1257, A:I.1261, B:L.200, B:L.204 Hydrogen bonds: B:C.215 3PE.12: 10 residues within 4Å: Chain A: N.277, G.279, F.280, M.282, L.283, V.635, C.638, I.642 Ligands: 3PE.18, 3PE.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.283 Hydrogen bonds: A:N.277, A:N.277 3PE.13: 10 residues within 4Å: Chain A: A.166, F.167, L.170, F.573, L.576, R.584, Y.627, P.633, I.639, I.643 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.167, A:L.170, A:F.573, A:L.576, A:I.639, A:I.643 Salt bridges: A:R.584 3PE.14: 11 residues within 4Å: Chain A: C.65, V.66, V.70, L.175, L.564, F.567, I.571, N.599, F.600, P.601 Ligands: 3PE.15 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.564, A:F.567 3PE.15: 9 residues within 4Å: Chain A: F.567, P.601, L.604, I.605, V.1039, E.1040, A.1042, I.1046 Ligands: 3PE.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.567, A:L.604, A:L.604, A:I.1046 3PE.18: 12 residues within 4Å: Chain A: F.205, I.208, N.277, F.278, G.279, M.1129, T.1132, G.1136, M.1137, H.1139, H.1141 Ligands: 3PE.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.205, A:I.208, A:F.278, A:F.278, A:F.278, A:T.1132 Hydrogen bonds: A:H.1141 Salt bridges: A:H.1139, A:H.1139 3PE.19: 11 residues within 4Å: Chain A: H.996, L.1001, S.1002, M.1005, Y.1358, Y.1359, I.1362, S.1363, M.1366, L.1367, F.1370 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.1005, A:Y.1358, A:Y.1359, A:Y.1359, A:M.1366, A:L.1367, A:F.1370, A:F.1370 Salt bridges: A:H.996 3PE.20: 15 residues within 4Å: Chain A: L.196, V.203, I.289, T.290, M.291, S.322, C.647, N.649, Y.650, I.651, L.653 Ligands: CA.10, 3PE.12, 4YH.22, 4YH.23 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.196, A:V.203, A:I.289, A:N.649, A:Y.650, A:I.651, A:L.653 Hydrogen bonds: A:T.290

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

PC1.16: 9 residues within 4Å: Chain A: Y.210, L.217, K.221, I.305, W.309, P.310, I.312, Y.313 Chain B: F.152 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.210, A:L.217, A:W.309, A:W.309, A:W.309 PC1.17: 12 residues within 4Å: Chain A: N.307, W.311, A.1271, I.1274, R.1302, T.1308, F.1309, P.1310, Q.1311, V.1313, L.1314, F.1317 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.311, A:W.311, A:A.1271, A:I.1274, A:F.1309, A:P.1310, A:V.1313, A:L.1314, A:F.1317, A:F.1317 Hydrogen bonds: A:N.307

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.21: 11 residues within 4Å: Chain A: L.326, L.330, S.334, L.657, L.664, F.1068, I.1372, I.1373, F.1376 Ligands: 4YH.22, 4YH.23 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.326, A:L.330, A:L.657, A:L.664, A:I.1372, A:F.1376

2 x 4YH: (2S)-2-(3,4-dimethoxyphenyl)-5-{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino}-2-(propan-2-yl)pentanenitrile(Non-covalent)

4YH.22: 15 residues within 4Å: Chain A: F.608, L.611, T.612, N.649, L.652, L.653, F.656, F.1013, I.1049, I.1050, A.1053, F.1060 Ligands: 3PE.20, 9Z9.21, 4YH.23 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.652, A:L.653, A:A.1053 pi-Stacking: A:F.1013 4YH.23: 13 residues within 4Å: Chain A: L.611, T.612, N.649, L.653, F.656, F.1013, A.1320, A.1369, I.1372, I.1373 Ligands: 3PE.20, 9Z9.21, 4YH.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.653, A:F.656, A:F.656

1 x ETA: ETHANOLAMINE(Covalent)

ETA.25: 3 residues within 4Å: Chain E: Q.374, Y.384, C.1045 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.1045

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 L-type calcium channel subunit beta-1: C
Voltage-dependent L-type calcium channel subunit beta-1: D
Voltage-dependent calcium channel subunit alpha-2/delta-1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
B

D
C

E
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 L-type calcium channel subunit beta-1

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

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

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