SMTL ID : 6jpb.1

Rabbit Cav1.1-Diltiazem Complex

Coordinates

PDB Format

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(Post Translational Modification)

NAG.8: 1 residues within 4Å: Chain A: N.257 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain E: N.298 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.298 NAG.20: 1 residues within 4Å: Chain E: N.862 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.862 NAG.21: 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.22: 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.23: 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.24: 1 residues within 4Å: Chain E: N.972 No protein-ligand interaction detected (PLIP) NAG.25: 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: 6 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322, E.1323 Ligands: CA.10 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.292, A:E.292, A:E.614, A:E.1014, A:E.1014 CA.10: 5 residues within 4Å: Chain A: E.292, E.614, E.1014, G.1322 Ligands: CA.9 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.292, A:E.1014 CA.17: 5 residues within 4Å: Chain A: D.78 Chain E: D.233, S.235, S.237, T.305 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:S.235, E:S.237, E:T.305

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

3PE.11: 7 residues within 4Å: Chain A: P.1181, W.1182, F.1185, R.1254, W.1258 Chain B: M.207, E.213 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.1181, A:W.1182, A:F.1185, A:R.1254 Hydrogen bonds: B:E.213 3PE.13: 11 residues within 4Å: Chain A: N.277, F.278, G.279, M.1129, T.1132, I.1133, G.1136, M.1137, H.1139, Y.1140, H.1141 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.278, A:T.1132, A:I.1133 Hydrogen bonds: A:N.277, A:G.279, A:H.1141 Salt bridges: A:H.1139, A:H.1139 3PE.14: 9 residues within 4Å: Chain A: L.522, S.525, V.526, C.529, I.945, L.949, R.1038, E.1040, M.1041 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.945, A:E.1040 Hydrogen bonds: A:L.522, A:S.525, A:S.525 Salt bridges: A:R.1038 3PE.15: 8 residues within 4Å: Chain A: T.936, L.1001, S.1002, M.1005, F.1008, Y.1358, Y.1359, M.1366 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1008, A:Y.1358, A:Y.1359, A:M.1366 Hydrogen bonds: A:Y.1358

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

PC1.12: 10 residues within 4Å: Chain A: Y.210, I.213, L.217, I.305, W.309, P.310, I.312, F.1234, L.1237, M.1241 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.210, A:I.213, A:W.309, A:W.309, A:W.309, A:I.312, A:F.1234, A:F.1234, A:L.1237

1 x C9F: Diltiazem(Non-covalent)

C9F.16: 8 residues within 4Å: Chain A: L.330, L.653, T.1012, F.1013, M.1057, A.1320, A.1369, F.1376 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.330, A:F.1013, A:A.1369, A:F.1376

1 x ETA: ETHANOLAMINE(Covalent)

ETA.18: 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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