SMTL ID : 8thh.1

Cryo-EM structure of Nav1.7 with LTG

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.1352, T.1354, F.1359, S.1377 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1365, N.1366, S.1368, E.1369, K.1423 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: F.54, Y.124, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

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

NAG.4: 2 residues within 4Å: Chain A: N.282, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.282, A:N.283, A:N.283 NAG.5: 1 residues within 4Å: Chain A: N.1375 No protein-ligand interaction detected (PLIP) NAG.22: 4 residues within 4Å: Chain B: V.91, N.93, R.96, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG.23: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.24: 3 residues within 4Å: Chain B: R.89, T.112, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114

2 x IYJ: (6M)-6-(2,3-dichlorophenyl)-1,2,4-triazine-3,5-diamine(Non-covalent)

IYJ.6: 11 residues within 4Å: Chain A: F.391, A.1403, T.1404, F.1405, K.1406, S.1445, T.1695, T.1696, S.1697, F.1748, V.1752 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1748 Hydrogen bonds: A:A.1403, A:T.1404, A:K.1406, A:S.1697 IYJ.7: 4 residues within 4Å: Chain A: A.402, M.403, L.968, L.1760 No protein-ligand interaction detected (PLIP)

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 3 residues within 4Å: Chain A: N.1256, A.1257, W.1260 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.1260 Y01.9: 11 residues within 4Å: Chain A: V.755, T.758, L.759, S.848, W.849, P.850, E.981, L.1326, I.1330, L.1333 Ligands: Y01.21 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.755, A:T.758, A:L.759, A:W.849, A:W.849, A:W.849, A:P.850, A:L.1326, A:L.1326, A:I.1330, A:L.1333 Hydrogen bonds: A:E.981 Y01.10: 9 residues within 4Å: Chain A: V.833, F.837, M.1338, Y.1429, S.1430, Y.1432, M.1433, I.1435, V.1439 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.833, A:V.833, A:F.837, A:Y.1432, A:I.1435, A:V.1439, A:V.1439 Y01.21: 11 residues within 4Å: Chain A: L.759, A.762, H.765, P.767, L.1329, L.1333, N.1391, G.1393, Y.1396 Ligands: Y01.9, PCW.12 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.759, A:A.762, A:L.1329, A:L.1333 Hydrogen bonds: A:N.1391 Salt bridges: A:H.765

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

LPE.11: 9 residues within 4Å: Chain A: N.1732, P.1733, S.1734, I.1737, F.1738, V.1741, S.1742, I.1745 Ligands: PCW.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1737, A:V.1741, A:I.1745, A:I.1745 LPE.13: 6 residues within 4Å: Chain A: A.1257, W.1258, L.1261, V.1311, N.1312, I.1315 No protein-ligand interaction detected (PLIP) LPE.17: 5 residues within 4Å: Chain A: Q.1478, Y.1481, P.1642, L.1644, F.1645 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1478 LPE.18: 9 residues within 4Å: Chain A: D.320, K.376, T.377, M.379, V.383, M.1655, G.1685, M.1688 Ligands: LPE.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.383 LPE.19: 10 residues within 4Å: Chain A: L.1203, S.1206, G.1207, A.1210, F.1211, M.1307, L.1649, F.1656, F.1684 Ligands: LPE.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1649, A:F.1656 Hydrogen bonds: A:A.1210 LPE.20: 6 residues within 4Å: Chain A: V.253, S.257, M.1529, M.1533, G.1626, A.1627 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.253

3 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.12: 7 residues within 4Å: Chain A: C.1328, L.1329, N.1391, G.1393, L.1400 Ligands: LPE.11, Y01.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1329, A:L.1400 Hydrogen bonds: A:N.1391 PCW.14: 11 residues within 4Å: Chain A: Y.339, G.340, Y.341, S.348, W.349, L.352, Q.941, A.942, L.945, M.949, M.950 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.349, A:L.352, A:A.942, A:L.945, A:L.945, A:M.949 Hydrogen bonds: A:Q.941 PCW.16: 12 residues within 4Å: Chain A: L.1488, K.1491, T.1575, G.1577, I.1580, F.1581, V.1584, V.1585, L.1614, I.1617, G.1618 Ligands: P5S.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1581, A:V.1585, A:I.1617 Salt bridges: A:K.1491

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.15: 16 residues within 4Å: Chain A: C.255, L.388, L.1488, G.1489, G.1577, W.1578, F.1581, L.1621, V.1624, R.1631, T.1632, L.1634, F.1635, L.1637, L.1641 Ligands: PCW.16 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.388, A:W.1578, A:F.1581, A:L.1621, A:V.1624, A:L.1634, A:L.1637, A:L.1641 Hydrogen bonds: A:G.1489, A:G.1489 Salt bridges: A:R.1631

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Dual-pocket inhibition of Na v channels by the antiepileptic drug lamotrigine. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-11-22

Peptides

Sodium channel protein type 9 subunit alpha: A
Sodium channel subunit beta-1: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

Sodium channel subunit beta-2

Related Entries With Identical Sequence