SMTL ID : 7yg5.1

Structure of human R-type voltage-gated CaV2.3-alpha2/delta1-beta1 channel complex in the topiramate-bound state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain C: E.567, F.894, N.895, F.982 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 8 residues within 4Å: Chain C: Q.108, W.113, E.115, N.468, T.470, K.480, N.481, L.485 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.480

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 8 residues within 4Å: Chain C: D.43, L.47, T.50, G.728, S.820, W.821, E.823, N.824 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.43

9 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 7 residues within 4Å: Chain A: L.1490, V.1494, P.1503, T.1505, Y.1506, A.1509 Ligands: R16.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1490, A:V.1494, A:P.1503, A:T.1505, A:Y.1506, A:Y.1506, A:Y.1506 Y01.9: 12 residues within 4Å: Chain A: W.557, R.561, T.564, F.566, F.1299, I.1302, F.1303, I.1306, R.1396, E.1398, M.1399, F.1402 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.557, A:F.566, A:F.1299, A:I.1302, A:F.1303, A:I.1306, A:F.1402, A:F.1402 Salt bridges: A:R.561, A:R.1396 Y01.11: 7 residues within 4Å: Chain A: A.494, I.495, H.497, N.499, F.1301, N.1357, I.1358 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.494, A:I.495, A:H.497, A:F.1301, A:N.1357, A:I.1358 Salt bridges: A:H.497, A:H.497 Y01.13: 9 residues within 4Å: Chain A: A.324, W.328, I.336, C.1611, F.1618, F.1650, L.1653, M.1654, F.1657 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.328, A:I.336, A:F.1618, A:F.1650, A:F.1657, A:F.1657 Y01.14: 6 residues within 4Å: Chain A: I.1168, E.1181, R.1182, V.1185, L.1186, F.1189 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.1185, A:L.1186, A:F.1189 Hydrogen bonds: A:E.1181 Y01.15: 13 residues within 4Å: Chain A: Q.223, L.226, F.229, L.233, M.1496, L.1586, Q.1589, G.1590, Y.1591, T.1592 Ligands: 3PE.8, Y01.16, Y01.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.226, A:L.226, A:F.229, A:F.229, A:F.229, A:L.233, A:L.1586 Hydrogen bonds: A:T.1592, A:T.1592 Y01.16: 9 residues within 4Å: Chain A: N.294, V.1493, M.1496, Y.1499, Y.1500, S.1501 Ligands: R16.5, 3PE.8, Y01.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1493, A:M.1496, A:Y.1499, A:Y.1499, A:Y.1499 Hydrogen bonds: A:S.1501 Y01.17: 6 residues within 4Å: Chain A: F.230, W.1542, L.1587, R.1594, L.1597, W.1598 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.230, A:L.1587, A:R.1594, A:L.1597, A:W.1598, A:W.1598 Y01.20: 5 residues within 4Å: Chain A: M.1485, A.1489, V.1493, Q.1589 Ligands: Y01.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.1489, A:V.1493, A:Q.1589

6 x R16: HEXADECANE(Non-covalent)

R16.5: 3 residues within 4Å: Chain A: Y.1506 Ligands: Y01.4, Y01.16 No protein-ligand interaction detected (PLIP) R16.6: 3 residues within 4Å: Chain A: G.159, W.160, K.212 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.160, A:W.160 R16.10: 3 residues within 4Å: Chain A: P.644, I.647, S.1400 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.644, A:P.644, A:I.647 R16.12: 4 residues within 4Å: Chain A: I.1359, W.1360, Y.1700, V.1704 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1359, A:W.1360, A:W.1360, A:Y.1700, A:V.1704 R16.21: 4 residues within 4Å: Chain A: G.225, V.299, I.684, L.688 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.684, A:L.688 R16.22: 6 residues within 4Å: Chain A: L.577, W.586, V.593, V.1295, F.1299, F.1413 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.577, A:W.586, A:W.586, A:V.1295, A:F.1299, A:F.1413, A:F.1413

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

3PE.7: 13 residues within 4Å: Chain A: F.242, Y.243, K.246, L.322, G.323, T.325, W.326, N.327, L.329, N.1571, S.1573, F.1574, L.1577 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.242, A:L.322, A:W.326, A:F.1574, A:L.1577 Hydrogen bonds: A:W.326, A:N.1571, A:S.1573 Salt bridges: A:K.246 3PE.8: 11 residues within 4Å: Chain A: Q.291, D.293, N.294, L.296, F.297, L.300, V.673, S.674, M.677 Ligands: Y01.15, Y01.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.296, A:L.296, A:L.300 Hydrogen bonds: A:Q.291, A:D.293, A:D.293, A:N.294

2 x CA: CALCIUM ION(Non-covalent)

CA.18: 3 residues within 4Å: Chain A: E.309, E.1372, G.1662 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.309, A:E.309, A:E.1372 CA.23: 4 residues within 4Å: Chain A: D.116 Chain C: S.261, S.263, T.331 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Metal complexes: A:D.116, C:S.261, C:S.263, C:T.331

1 x TOR: [(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate(Non-covalent)

TOR.19: 13 residues within 4Å: Chain A: V.210, S.213, F.354, E.357, N.363, S.599, S.602, I.603, L.606, A.700, I.701, D.704, N.705 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.210, A:E.357, A:L.606, A:D.704 Hydrogen bonds: A:S.213, A:S.599, A:S.602, A:S.602, A:D.704, A:N.705

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

NAG.24: 3 residues within 4Å: Chain C: L.89, N.92, E.199 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.89 Hydrogen bonds: C:N.92, C:E.199, C:E.199 NAG.25: 1 residues within 4Å: Chain C: N.324 No protein-ligand interaction detected (PLIP) NAG.26: 2 residues within 4Å: Chain C: N.346, N.348 No protein-ligand interaction detected (PLIP) NAG.27: 3 residues within 4Å: Chain C: T.587, R.589, N.604 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.587 Hydrogen bonds: C:R.589, C:N.604 NAG.28: 4 residues within 4Å: Chain C: E.80, A.83, R.84, N.613 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.80, C:A.83 Hydrogen bonds: C:N.613 NAG.29: 3 residues within 4Å: Chain C: N.675, T.677, E.678 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.675, C:T.677 NAG.30: 1 residues within 4Å: Chain C: N.888 No protein-ligand interaction detected (PLIP) NAG.31: 5 residues within 4Å: Chain C: V.107, R.114, E.121, N.184, W.185 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.107 Hydrogen bonds: C:R.114, C:R.114, C:E.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, Y. et al., Structural insights into the allosteric effects of the antiepileptic drug topiramate on the Ca V 2.3 channel. Biochem.Biophys.Res.Commun. (2024)

Release Date

2023-11-29

Peptides

Voltage-dependent R-type calcium channel subunit alpha-1E: A
Voltage-dependent L-type calcium channel subunit beta-1: B
Voltage-dependent calcium channel subunit alpha-2/delta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Voltage-dependent R-type calcium channel subunit alpha-1E

Voltage-dependent L-type calcium channel subunit beta-1

Voltage-dependent calcium channel subunit alpha-2/delta-1

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