SMTL ID : 7wlj.1

CryoEM structure of human low-voltage activated T-type calcium channel Cav3.3 in complex with mibefradil (MIB)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x MWV: (1S,2S)-2-(2-{[3-(1H-benzimidazol-2-yl)propyl](methyl)amino}ethyl)-6-fluoro-1-(propan-2-yl)-1,2,3,4-tetrahydronaphthalen-2-yl methoxyacetate(Non-covalent)

MWV.1: 16 residues within 4Å: Chain A: F.387, N.391, L.394, F.815, L.818, T.819, N.850, F.854, K.1379, S.1419, V.1422, Q.1718, L.1721, I.1722, V.1725 Ligands: 3PE.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.394, A:F.815, A:F.815, A:T.819, A:F.854, A:I.1722, A:V.1725 Hydrogen bonds: A:N.850, A:K.1379 pi-Stacking: A:F.854

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

3PE.2: 12 residues within 4Å: Chain A: C.1313, F.1374, A.1377, S.1378, V.1422, M.1425, L.1715, Q.1718, F.1719, I.1722 Ligands: MWV.1, Y01.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1374, A:Q.1718, A:F.1719, A:I.1722 Hydrogen bonds: A:S.1378 Salt bridges: A:K.1379 3PE.3: 4 residues within 4Å: Chain A: I.383, G.1623, T.1676, L.1721 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.383, A:T.1676, A:L.1721 3PE.5: 2 residues within 4Å: Chain A: F.1495, C.1498 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1495, A:F.1495, A:F.1495 3PE.6: 3 residues within 4Å: Chain A: L.214, F.217, C.1498 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.214, A:F.217 3PE.7: 2 residues within 4Å: Chain A: N.1404, M.1407 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.357, E.821, D.822, D.1380 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.357

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 8 residues within 4Å: Chain A: I.222, F.223, I.226, L.230, S.371, Y.373, N.374, Y.377 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.222, A:F.223, A:F.223, A:I.226, A:I.226, A:L.230, A:Y.373, A:Y.377 Salt bridges: A:H.370 Y01.9: 6 residues within 4Å: Chain A: T.654, V.655, I.659, H.661, N.1365, L.1366 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.654, A:V.655, A:N.1365 Salt bridges: A:H.661 Y01.11: 8 residues within 4Å: Chain A: I.783, T.834, S.835, W.837, A.838, L.840, Y.841, F.848 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.783, A:A.838, A:L.840, A:Y.841, A:F.848 Hydrogen bonds: A:S.835 Y01.13: 9 residues within 4Å: Chain A: F.372, F.375, M.1627, H.1658, G.1665, F.1668, L.1669, F.1672 Ligands: Y01.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.372, A:F.375, A:F.1668, A:F.1668, A:L.1669, A:F.1672 Y01.14: 7 residues within 4Å: Chain A: A.1188, L.1189, F.1631, N.1663, F.1664, G.1665 Ligands: Y01.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.1188, A:L.1189, A:F.1631, A:F.1664 Salt bridges: A:R.1191 Y01.15: 9 residues within 4Å: Chain A: F.1317, G.1367, Q.1368, M.1371, F.1374, Q.1703, F.1704, P.1707 Ligands: 3PE.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.1317, A:Q.1368, A:M.1371, A:F.1374, A:F.1374, A:F.1704, A:F.1704, A:P.1707

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

NAG.10: 3 residues within 4Å: Chain A: N.1345, S.1347, D.1348 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain A: D.1339, R.1341, N.1342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, L. et al., Structure, gating, and pharmacology of human Ca V 3.3 channel. Nat Commun (2022)

Release Date

2022-05-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

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

Voltage-dependent T-type calcium channel subunit alpha-1I

Related Entries With Identical Sequence