SMTL ID : 7wll.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x 1II: 3-[1-[4,4-bis(4-fluorophenyl)butyl]piperidin-4-yl]-1~{H}-benzimidazol-2-one(Non-covalent)

1II.1: 18 residues within 4Å: Chain A: F.387, N.391, L.394, L.818, T.819, Q.820, N.850, F.854, V.858, K.1379, S.1419, L.1423, F.1426, Q.1718, L.1721, I.1722, V.1725 Ligands: 3PE.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.394, A:T.819, A:F.854, A:V.858, A:L.1423, A:I.1722 Hydrogen bonds: A:L.818 Halogen bonds: A:L.1423

9 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)(Non-functional Binders)

3PE.2: 12 residues within 4Å: Chain A: V.1310, A.1377, S.1378, K.1379, V.1422, L.1715, Q.1718, F.1719, I.1722 Ligands: 1II.1, CA.6, Y01.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1310, A:V.1422, A:L.1715, A:L.1715, A:F.1719 Salt bridges: A:K.1379 3PE.3: 4 residues within 4Å: Chain A: I.382, F.388, F.1626, L.1721 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.382, A:F.1626, A:F.1626, A:L.1721 3PE.4: 2 residues within 4Å: Chain A: I.1491, F.1495 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1491, A:F.1495, A:F.1495 3PE.5: 2 residues within 4Å: Chain A: L.214, C.1498 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.214 3PE.10: 1 residues within 4Å: Ligands: 3PE.16 No protein-ligand interaction detected (PLIP) 3PE.16: 3 residues within 4Å: Chain A: V.729, T.732 Ligands: 3PE.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.729 3PE.18: 6 residues within 4Å: Chain A: L.808, I.811, P.1405, W.1406, L.1409, I.1412 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.808, A:I.811, A:P.1405, A:W.1406, A:W.1406, A:L.1409, A:I.1412 3PE.20: 7 residues within 4Å: Chain A: G.344, W.347, I.348, P.836, W.837, S.839, V.843 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.347, A:I.348, A:I.348, A:W.837, A:V.843, A:V.843 3PE.21: 6 residues within 4Å: Chain A: C.766, F.854, L.857, L.1416, S.1419, F.1420 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.854, A:L.857, A:L.1416, A:F.1420, A:F.1420

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.357, Q.820, K.1379, G.1677 Ligands: 3PE.2 No protein-ligand interaction detected (PLIP) CA.7: 3 residues within 4Å: Chain A: E.357, E.821, D.1380 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.357, A:E.357

7 x Y01: CHOLESTEROL HEMISUCCINATE(Covalent)(Non-covalent)

Y01.8: 12 residues within 4Å: Chain A: F.223, I.226, L.230, N.275, H.370, S.371, Y.373, N.374, I.376, Y.377, L.380, R.1585 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.223, A:I.226, A:I.226, A:L.230, A:I.376, A:Y.377 Hydrogen bonds: A:S.371 Salt bridges: A:H.370, A:R.1585 Y01.11: 7 residues within 4Å: Chain A: V.655, G.658, H.661, N.1365, L.1366, G.1367 Ligands: Y01.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.655, A:H.661, A:N.1365, A:L.1366 Salt bridges: A:H.661 Y01.12: 10 residues within 4Å: Chain A: C.1314, N.1365, G.1367, Q.1368, F.1374, Q.1703, P.1707, V.1711 Ligands: 3PE.2, Y01.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1374, A:P.1707, A:V.1711 Hydrogen bonds: A:N.1365 Y01.14: 6 residues within 4Å: Chain A: T.834, S.835, W.837, A.838, L.840, Y.841 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.838, A:L.840 Hydrogen bonds: A:S.835 Y01.15: 7 residues within 4Å: Chain A: F.372, F.375, I.379, M.1666, F.1668, L.1669 Ligands: Y01.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.372, A:F.375, A:I.379, A:F.1668, A:F.1668, A:F.1668, A:L.1669, A:L.1669 Y01.17: 9 residues within 4Å: Chain A: F.1181, I.1185, A.1188, R.1191, F.1631, N.1663, F.1664, G.1665 Ligands: Y01.15 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.1181, A:F.1181, A:F.1181, A:I.1185, A:I.1185, A:A.1188, A:F.1631, A:F.1664 Salt bridges: A:R.1191 Y01.19: 6 residues within 4Å: Chain A: C.93, V.94, M.98, M.195, M.770, S.806 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: D.1339, R.1341, N.1342 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.1341, A:N.1342 NAG.13: 3 residues within 4Å: Chain A: N.1345, S.1347, D.1348 No protein-ligand interaction detected (PLIP)

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

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