SMTL ID : 8thg.1

Cryo-EM structure of Nav1.7 with RLZ

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: 5 residues within 4Å: Chain A: N.1352, T.1354, D.1355, S.1377, V.1380 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1365, N.1366, S.1368, E.1369 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: F.54, R.72, 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.283 NAG.5: 1 residues within 4Å: Chain A: N.1375 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: V.91, N.93, R.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.93, B:R.96, B:R.96 NAG.19: 2 residues within 4Å: Chain B: G.33, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:N.110 NAG.20: 4 residues within 4Å: Chain B: E.84, R.85, R.89, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114

1 x 657: 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine(Non-covalent)

657.6: 9 residues within 4Å: Chain A: Q.360, F.391, T.1404, T.1695, T.1696, S.1697, I.1744, S.1747, F.1748 No protein-ligand interaction detected (PLIP)

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 8 residues within 4Å: Chain A: V.755, L.759, L.845, S.848, W.849, L.1326, I.1330 Ligands: Y01.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.755, A:L.759, A:L.845, A:W.849, A:W.849, A:W.849 Y01.8: 10 residues within 4Å: Chain A: V.833, F.837, M.1338, Y.1429, S.1430, Y.1432, M.1433, I.1435, Y.1436, V.1439 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.833, A:V.833, A:F.837, A:Y.1432, A:I.1435, A:I.1435, A:Y.1436, A:V.1439 Y01.17: 10 residues within 4Å: Chain A: A.762, H.765, P.767, L.1329, L.1333, N.1391, V.1392, G.1393, Y.1396 Ligands: Y01.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.762, A:L.1329, A:L.1333, A:V.1392 Hydrogen bonds: A:N.1391 Salt bridges: A:H.765

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

LPE.9: 7 residues within 4Å: Chain A: N.1732, P.1733, S.1734, I.1737, F.1738, V.1741, S.1742 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1737, A:F.1738, A:V.1741 Hydrogen bonds: A:N.1732 LPE.10: 5 residues within 4Å: Chain A: A.1257, W.1258, R.1308, V.1311, N.1312 No protein-ligand interaction detected (PLIP) LPE.13: 6 residues within 4Å: Chain A: T.1475, E.1477, Q.1478, L.1644, F.1645, M.1754 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1645 Hydrogen bonds: A:Q.1478 LPE.14: 8 residues within 4Å: Chain A: T.319, D.320, K.376, T.377, F.1652, M.1655, M.1688, I.1689 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1652, A:M.1688 Hydrogen bonds: A:K.376 Salt bridges: A:D.320, A:K.376 LPE.15: 7 residues within 4Å: Chain A: S.1206, A.1210, F.1211, K.1219, I.1222, L.1653, F.1656 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1653 Salt bridges: A:K.1219 LPE.16: 2 residues within 4Å: Chain A: S.257 Ligands: PCW.11 No protein-ligand interaction detected (PLIP)

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

PCW.11: 14 residues within 4Å: Chain A: Y.339, Y.341, S.348, W.349, F.351, L.352, F.355, Q.941, A.942, L.945, I.946, M.949, M.950 Ligands: LPE.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.349, A:F.351, A:L.352, A:F.355, A:L.945, A:L.945, A:I.946, A:M.949 Hydrogen bonds: A:S.348

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

P5S.12: 13 residues within 4Å: Chain A: C.255, L.388, G.1489, G.1577, W.1578, F.1581, L.1621, V.1624, K.1628, R.1631, T.1632, L.1634, F.1635 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.388, A:W.1578, A:F.1581, A:F.1581, A:L.1621, A:V.1624, A:L.1634, A:L.1634 Hydrogen bonds: 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.
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Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

Sodium channel subunit beta-2

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