SMTL ID : 9ayk.1

Cryo-EM structure of human Cav3.2 with ML218

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x 01: 3,5-dichloro-N-{[(1R,5S,6r)-3-(3,3-dimethylbutyl)-3-azabicyclo[3.1.0]hexan-6-yl]methyl}benzamide

01.1: 10 residues within 4Å: Chain A: L.685, F.731, L.734, T.735, G.765, N.766, F.770, K.1266, F.1313 Ligands: JL3.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.685, A:L.734, A:F.770, A:F.1313 Hydrogen bonds: A:L.734 Halogen bonds: A:G.765

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.2: 2 residues within 4Å: Chain A: D.306, N.388 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.388 NAG.3: 1 residues within 4Å: Chain A: N.1229 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: E.421, E.737, D.1267 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.421, A:D.1267

1 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.5: 12 residues within 4Å: Chain A: F.436, Y.437, F.439, I.443, M.1520, N.1556, G.1558, M.1559, F.1561, L.1562, F.1565 Ligands: Y01.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.439, A:I.443, A:F.1561, A:F.1561, A:L.1562, A:F.1565, A:F.1565 Hydrogen bonds: A:N.1556 pi-Cation interactions: A:F.436

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 9 residues within 4Å: Chain A: V.1072, A.1075, L.1076, R.1078, D.1080, F.1524, N.1556, F.1557 Ligands: LPE.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.1072, A:A.1075, A:L.1076, A:F.1524, A:N.1556, A:F.1557 Salt bridges: A:R.1078 Y01.8: 5 residues within 4Å: Chain A: N.406, I.407, S.1398, H.1401 Ligands: JL3.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.406, A:I.407, A:H.1401 Y01.12: 6 residues within 4Å: Chain A: L.571, G.574, V.575, Y.577, I.1205, L.1253 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.571, A:V.575, A:Y.577, A:Y.577, A:I.1205 Y01.13: 11 residues within 4Å: Chain A: F.1204, G.1254, Q.1255, L.1257, M.1258, S.1593, Y.1594, A.1597, P.1600, V.1604 Ligands: JL3.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1204, A:L.1257, A:M.1258, A:P.1600, A:V.1604

4 x JL3: [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate(Non-covalent)

JL3.7: 13 residues within 4Å: Chain A: F.284, N.406, G.408, Y.409, W.411, I.412, S.751, S.752, W.753, L.756, V.759 Ligands: Y01.8, JL3.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.284, A:F.284, A:F.284, A:W.411, A:W.411, A:I.412, A:W.753, A:W.753, A:L.756, A:V.759 Hydrogen bonds: A:S.751, A:S.752 JL3.9: 6 residues within 4Å: Chain A: L.699, S.749, T.750, S.751, Y.757 Ligands: JL3.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.699 JL3.10: 11 residues within 4Å: Chain A: C.1201, S.1264, K.1266, V.1309, M.1312, T.1569, L.1608, Q.1611, F.1612 Ligands: 01.1, Y01.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1309, A:F.1612, A:F.1612 Hydrogen bonds: A:T.1569, A:Q.1611 Salt bridges: A:K.1266 JL3.11: 5 residues within 4Å: Chain A: T.648, K.1218, N.1291, M.1294, Y.1297 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.648 Hydrogen bonds: A:K.1218, A:K.1218, A:N.1291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Structural basis for human Ca v 3.2 inhibition by selective antagonists. Cell Res. (2024)

Release Date

2024-04-24

Peptides

Voltage-dependent T-type calcium channel subunit alpha-1H: 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-1H

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