SMTL ID : 8s9c.1

Cryo-EM structure of Nav1.7 with CBZ

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, F.1359, S.1377 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: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.282, A:N.283 NAG.5: 1 residues within 4Å: Chain A: N.1375 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain B: V.91, N.93, R.96, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.96, B:R.96 NAG.29: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.30: 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

1 x N6W: benzo[b][1]benzazepine-11-carboxamide(Non-covalent)

N6W.6: 8 residues within 4Å: Chain A: A.402, L.967, L.968, F.971, S.972, I.1457, N.1461, L.1760 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.402, A:L.967, A:L.968, A:F.971, A:I.1457, A:L.1760 Hydrogen bonds: A:N.1461

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

P5S.7: 10 residues within 4Å: Chain A: W.1179, R.1182, Y.1186, W.1245, I.1246, A.1247, G.1249, Y.1250, T.1252 Ligands: LPE.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.1246, A:Y.1250, A:Y.1250 Salt bridges: A:R.1182, A:R.1182, A:K.1183, A:K.1251 P5S.16: 14 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 Ligands: PCW.17 10 PLIP interactions: 10 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.1634 Hydrogen bonds: A:G.1489, A:G.1489 Salt bridges: A:R.1631 P5S.25: 5 residues within 4Å: Chain A: L.1566, I.1567, R.1570, H.1571 Ligands: PCW.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1566 Salt bridges: A:H.1571

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 4 residues within 4Å: Chain A: N.1256, A.1257, W.1260 Ligands: Y01.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.1260 Y01.9: 7 residues within 4Å: Chain A: W.1245, K.1251, F.1254, T.1255, W.1260, F.1263 Ligands: Y01.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1245, A:K.1251, A:F.1254, A:F.1254, A:W.1260, A:F.1263 Y01.10: 8 residues within 4Å: Chain A: V.755, T.758, L.759, S.848, W.849, P.850, I.1330, L.1333 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.755, A:V.755, A:T.758, A:L.759, A:W.849, A:I.1330, A:L.1333 Y01.11: 9 residues within 4Å: Chain A: V.833, M.1338, L.1342, Y.1429, S.1430, Y.1432, M.1433, I.1435, V.1439 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.833, A:V.833, A:L.1342, A:L.1342, A:Y.1429, A:Y.1432, A:V.1439, A:V.1439 Hydrogen bonds: A:Y.1429 Y01.26: 9 residues within 4Å: Chain A: A.762, H.765, P.767, L.1329, L.1333, N.1391, G.1393, Y.1396 Ligands: PCW.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.762, A:L.1329, A:L.1333 Hydrogen bonds: A:N.1391 Salt bridges: A:H.765

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

LPE.12: 7 residues within 4Å: Chain A: P.1733, S.1734, I.1737, F.1738, S.1742, I.1745 Ligands: PCW.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1738, A:I.1745, A:I.1745 LPE.14: 5 residues within 4Å: Chain A: A.1257, W.1258, L.1261, N.1312, I.1315 No protein-ligand interaction detected (PLIP) LPE.18: 7 residues within 4Å: Chain A: E.1477, Q.1478, Y.1481, P.1642, L.1644, F.1645 Ligands: LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.1478 Salt bridges: A:E.1477 LPE.19: 5 residues within 4Å: Chain A: Y.1481, A.1484, M.1485 Ligands: PCW.17, LPE.18 No protein-ligand interaction detected (PLIP) LPE.20: 9 residues within 4Å: Chain A: D.320, K.376, T.377, M.379, V.383, F.1652, M.1655, G.1685, M.1688 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.383, A:F.1652 LPE.21: 9 residues within 4Å: Chain A: L.1203, S.1206, G.1207, A.1210, F.1211, M.1307, L.1649, L.1653, F.1684 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1203, A:L.1649, A:L.1653 Hydrogen bonds: A:A.1210 LPE.22: 3 residues within 4Å: Chain A: S.257, M.1529, A.1627 No protein-ligand interaction detected (PLIP) LPE.23: 5 residues within 4Å: Chain A: W.1178, W.1179, R.1182, Y.1250 Ligands: P5S.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1182 LPE.27: 9 residues within 4Å: Chain A: K.1187, I.1188, H.1191, F.1194, F.1197 Chain B: W.173, L.174, E.177, C.181 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:E.177 pi-Cation interactions: A:H.1191

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

PCW.13: 9 residues within 4Å: Chain A: L.1325, C.1328, L.1329, G.1393, Y.1396, V.1741, I.1745 Ligands: LPE.12, Y01.26 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1325, A:L.1325, A:L.1329, A:L.1329, A:Y.1396, A:V.1741, A:I.1745 PCW.15: 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.17: 13 residues within 4Å: Chain A: L.1488, K.1491, T.1575, G.1577, I.1580, F.1581, V.1584, L.1614, I.1617, G.1618, M.1638 Ligands: P5S.16, LPE.19 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1581, A:F.1581, A:V.1584, A:I.1617 Salt bridges: A:K.1491 PCW.24: 6 residues within 4Å: Chain A: F.1583, V.1584, I.1587, I.1588, V.1591 Ligands: P5S.25 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1583, A:F.1583, A:V.1584, A:I.1587, A:I.1588, A:V.1591

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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