SMTL ID : 6kzp.1

calcium channel-ligand

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: E.373, E.808, D.1348 Ligands: CA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.373, A:E.373, A:E.808, A:D.1348 CA.2: 5 residues within 4Å: Chain A: E.373, Q.807, E.808, G.1663 Ligands: CA.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.373

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

NAG.3: 1 residues within 4Å: Chain A: N.265 No protein-ligand interaction detected (PLIP) NAG.4: 5 residues within 4Å: Chain A: F.261, P.263, E.264, N.341, S.343 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.264, A:S.343 NAG.5: 2 residues within 4Å: Chain A: D.1307, N.1310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1310 NAG.6: 3 residues within 4Å: Chain A: T.1312, N.1313, S.1315 No protein-ligand interaction detected (PLIP)

1 x DZR: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide(Non-covalent)

DZR.7: 9 residues within 4Å: Chain A: L.410, F.802, L.805, T.806, G.836, N.837, F.841, K.1347 Ligands: 3PE.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.410, A:F.841 Hydrogen bonds: A:T.806, A:N.837, A:K.1347

8 x 3PE: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE(Non-covalent)(Non-functional Binders)

3PE.8: 7 residues within 4Å: Chain A: F.388, Y.389, R.1648, N.1649, G.1651, M.1652, L.1655 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.389 Hydrogen bonds: A:R.1648, A:N.1649 3PE.9: 6 residues within 4Å: Chain A: N.358, G.360, W.363, A.1491, H.1494 Ligands: 3PE.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.358 Salt bridges: A:H.1494 3PE.10: 8 residues within 4Å: Chain A: F.241, G.360, Y.361, W.363, I.364, S.823, I.830 Ligands: 3PE.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.241, A:Y.361, A:W.363, A:I.364, A:I.364, A:I.830 3PE.11: 9 residues within 4Å: Chain A: L.767, L.771, K.775, S.820, T.821, S.822, W.824, A.825, A.831 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.767, A:L.771, A:A.831 Hydrogen bonds: A:T.821 Salt bridges: A:K.775 3PE.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.13: 9 residues within 4Å: Chain A: C.1282, V.1390, T.1662, L.1698, Q.1701, F.1702, V.1705 Ligands: DZR.7, Y01.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1390, A:F.1702, A:F.1702 3PE.14: 10 residues within 4Å: Chain A: I.761, L.795, I.798, V.799, F.802, P.1373, W.1374, L.1376, L.1377, I.1380 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.761, A:L.795, A:I.798, A:V.799, A:F.802, A:F.802, A:P.1373, A:W.1374, A:W.1374, A:W.1374, A:L.1376, A:L.1377, A:I.1380 3PE.15: 9 residues within 4Å: Chain A: V.717, T.720, F.721, M.724, F.1288, L.1291, N.1372, M.1375, S.1381 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.717, A:T.720, A:F.721, A:F.1288, A:L.1291, A:L.1291

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.16: 7 residues within 4Å: Chain A: I.647, Y.649, N.1333, L.1334, G.1335, L.1338 Ligands: Y01.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.647, A:Y.649, A:N.1333, A:L.1334, A:L.1338 Y01.17: 13 residues within 4Å: Chain A: F.1285, R.1326, N.1333, G.1335, Q.1336, L.1338, M.1339, F.1342, T.1686, P.1690, V.1694 Ligands: 3PE.13, Y01.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.1285, A:F.1285, A:L.1338, A:F.1342, A:F.1342, A:P.1690, A:V.1694 Hydrogen bonds: A:N.1333, A:Q.1336 Salt bridges: A:R.1326 Y01.18: 12 residues within 4Å: Chain A: I.243, F.244, V.247, L.251, E.295, N.296, H.386, S.387, Y.389, N.390, I.392, Y.393 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.243, A:F.244, A:F.244, A:V.247, A:V.247, A:L.251, A:Y.389, A:I.392 Hydrogen bonds: A:N.296 Salt bridges: A:H.386

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Cryo-EM structures of apo and antagonist-bound human Cav3.1. Nature (2019)

Release Date

2019-12-18

Peptides

Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent T-type calcium channel subunit alpha-1G,Voltage-dependent T-type calcium channel subunit alpha-1G