SMTL ID : 8s9b.1

Cryo-EM structure of Nav1.7 with LCM

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, D.1355, 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: 5 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

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

NAG.4: 1 residues within 4Å: Chain A: N.1375 No protein-ligand interaction detected (PLIP) NAG.24: 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.25: 3 residues within 4Å: Chain B: G.33, R.89, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:R.89 NAG.26: 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 LQO: lacosamide(Non-covalent)

LQO.5: 13 residues within 4Å: Chain A: T.359, Q.360, I.394, K.1406, T.1695, T.1696, S.1697, A.1698, I.1744, S.1747, F.1748, V.1751, V.1752 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.1698, A:V.1751 Hydrogen bonds: A:K.1406, A:T.1696, A:T.1696 LQO.6: 5 residues within 4Å: Chain A: A.402, E.406, L.967, L.968, L.1760 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.402, A:L.967, A:L.968, A:L.1760 Hydrogen bonds: A:E.406

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

P5S.7: 12 residues within 4Å: Chain A: W.1178, W.1179, R.1182, Y.1186, W.1245, I.1246, A.1247, Y.1248, G.1249, Y.1250, K.1251 Ligands: LPE.21 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1178, A:I.1246, A:Y.1250, A:Y.1250 Salt bridges: A:R.1182, A:R.1182, A:K.1251 P5S.14: 13 residues within 4Å: Chain A: F.254, C.255, L.1488, G.1489, G.1577, W.1578, F.1581, R.1631, L.1634, F.1635, L.1637, M.1638 Ligands: PCW.15 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.254, A:W.1578, A:W.1578, A:W.1578, A:F.1581, A:L.1634, A:L.1634, A:L.1637, A:M.1638 Salt bridges: A:R.1631

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 5 residues within 4Å: Chain A: F.1254, T.1255, N.1256, A.1257, W.1260 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1260, A:W.1260 Y01.9: 10 residues within 4Å: Chain A: V.755, T.758, L.759, V.842, S.848, W.849, P.850, L.1326, I.1330, L.1333 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.755, A:T.758, A:L.759, A:V.842, A:W.849, A:P.850, A:I.1330, A:L.1333 Y01.10: 9 residues within 4Å: Chain A: V.833, F.837, M.1338, Y.1429, S.1430, Y.1432, M.1433, I.1435, Y.1436 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.833, A:V.833, A:Y.1432, A:I.1435, A:Y.1436 Y01.23: 11 residues within 4Å: Chain A: L.759, A.762, H.765, P.767, L.1329, I.1330, L.1333, N.1391, V.1392, G.1393, Y.1396 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.759, A:A.762, A:P.767, A:L.1329, A:I.1330, A:L.1333, A:V.1392 Hydrogen bonds: A:N.1391 Salt bridges: A:H.765, A:H.765

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

LPE.11: 7 residues within 4Å: Chain A: P.1733, S.1734, I.1737, F.1738, V.1741, S.1742, I.1745 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1737, A:F.1738, A:V.1741, A:I.1745, A:I.1745 LPE.12: 5 residues within 4Å: Chain A: A.1257, W.1258, V.1311, N.1312, I.1315 No protein-ligand interaction detected (PLIP) LPE.16: 7 residues within 4Å: Chain A: E.1477, Q.1478, Y.1481, L.1641, P.1642, L.1644, F.1645 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1641, A:F.1645 Hydrogen bonds: A:Q.1478 Salt bridges: A:E.1477 LPE.17: 4 residues within 4Å: Chain A: Y.1481, A.1484, M.1485 Ligands: PCW.15 No protein-ligand interaction detected (PLIP) LPE.18: 7 residues within 4Å: Chain A: D.320, K.376, T.377, M.379, M.1655, G.1685 Ligands: LPE.19 No protein-ligand interaction detected (PLIP) LPE.19: 10 residues within 4Å: Chain A: S.1206, G.1207, A.1210, F.1211, M.1307, L.1649, L.1653, F.1656, F.1684 Ligands: LPE.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1649, A:L.1653, A:F.1656 Hydrogen bonds: A:A.1210 LPE.20: 5 residues within 4Å: Chain A: V.253, S.257, M.1529, M.1533, A.1627 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.253 LPE.21: 6 residues within 4Å: Chain A: W.1178, W.1179, R.1182, W.1245, Y.1250 Ligands: P5S.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.1245 Hydrogen bonds: A:R.1182

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

PCW.13: 11 residues within 4Å: Chain A: Y.339, G.340, Y.341, S.348, W.349, F.351, Q.941, A.942, L.945, M.949, M.950 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.349, A:F.351, A:A.942, A:L.945, A:L.945, A:M.949 Hydrogen bonds: A:Q.941 PCW.15: 14 residues within 4Å: Chain A: L.1488, K.1491, Q.1494, T.1575, V.1576, G.1577, F.1581, V.1584, I.1588, L.1614, G.1618, M.1638 Ligands: P5S.14, LPE.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1581, A:V.1584 Hydrogen bonds: A:G.1577 Salt bridges: A:K.1491 PCW.22: 5 residues within 4Å: Chain A: F.1574, I.1580, V.1584, I.1587, I.1588 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1574, A:I.1580, A:I.1580, A:V.1584, A:I.1587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Q. et al., Structural mapping of Na v 1.7 antagonists. Nat Commun (2023)

Release Date

2023-08-30

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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