SMTL ID : 8g1a.1

Cryo-EM structure of Nav1.7 with CBD

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 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: 6 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, L.126, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

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

NAG.3: 2 residues within 4Å: Chain A: N.282, N.283 No protein-ligand interaction detected (PLIP) NAG.4: 5 residues within 4Å: Chain A: P.1365, N.1366, S.1368, E.1369, K.1423 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.1423 NAG.5: 1 residues within 4Å: Chain A: N.1375 No protein-ligand interaction detected (PLIP) NAG.31: 3 residues within 4Å: Chain B: V.91, N.93, F.107 No protein-ligand interaction detected (PLIP) NAG.32: 3 residues within 4Å: Chain B: G.33, T.109, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.33: 4 residues within 4Å: Chain B: R.85, R.89, T.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.112 Hydrogen bonds: B:N.114

2 x P0T: cannabidiol(Non-covalent)

P0T.6: 11 residues within 4Å: Chain A: A.1313, L.1314, A.1317, I.1321, N.1459, F.1460, Q.1463, L.1749, N.1753, I.1756, L.1760 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1314, A:A.1317, A:I.1321, A:F.1460, A:L.1749, A:L.1749, A:I.1756, A:I.1756, A:L.1760 P0T.7: 12 residues within 4Å: Chain A: V.383, I.386, F.387, F.391, L.1651, F.1692, T.1695, T.1696, V.1751, M.1754 Ligands: LPE.23, LPE.24 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.383, A:F.387, A:F.387, A:F.391, A:L.1651, A:F.1692, A:F.1692, A:T.1695, A:V.1751, A:V.1751

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

P5S.8: 13 residues within 4Å: Chain A: W.1179, R.1182, Y.1186, L.1242, W.1245, I.1246, A.1247, Y.1248, G.1249, Y.1250, K.1251 Ligands: LPE.27, LPE.28 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1242, A:I.1246, A:Y.1250 Hydrogen bonds: A:K.1251 Salt bridges: A:R.1182, A:R.1182, A:K.1251 P5S.21: 13 residues within 4Å: Chain A: L.388, G.1489, G.1577, W.1578, F.1581, L.1621, V.1624, R.1631, T.1632, L.1634, L.1637, M.1638 Ligands: PCW.22 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.388, A:L.388, A:W.1578, A:W.1578, A:W.1578, A:F.1581, A:L.1621, A:V.1624, A:L.1634, A:L.1634, A:L.1637 Hydrogen bonds: A:G.1489 Salt bridges: A:R.1631

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 2 residues within 4Å: Chain A: A.1257, W.1260 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1257, A:W.1260, A:W.1260, A:W.1260 Y01.10: 10 residues within 4Å: Chain A: V.755, T.758, L.759, S.848, W.849, E.981, L.988, L.1326, I.1330, L.1333 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.755, A:V.755, A:T.758, A:L.759, A:W.849, A:W.849, A:W.849, A:L.988, A:L.1326, A:L.1333 Y01.12: 11 residues within 4Å: Chain A: A.212, T.215, L.219, L.222, V.235, I.876, F.880, L.887, M.943, M.950, I.954 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.212, A:T.215, A:L.219, A:V.235, A:I.876, A:F.880, A:L.887, A:I.954 Y01.13: 2 residues within 4Å: Chain A: Y.1432, V.1439 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1432, A:Y.1432, A:V.1439 Y01.30: 9 residues within 4Å: Chain A: A.762, H.765, P.767, L.1329, L.1333, N.1391 Ligands: LPE.14, LPE.16, PCW.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1329, A:L.1333 Salt bridges: A:H.765

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.11: 11 residues within 4Å: Chain A: N.395, L.398, E.406, F.963, L.964, L.967, S.972, I.1453, I.1457, I.1759, F.1763 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.398, A:F.963, A:L.967, A:I.1453, A:I.1453, A:I.1457, A:I.1759, A:I.1759, A:F.1763 Hydrogen bonds: A:E.406

13 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

LPE.14: 5 residues within 4Å: Chain A: M.763, H.765, F.772 Ligands: LPE.16, Y01.30 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.765 LPE.15: 8 residues within 4Å: Chain A: P.1733, S.1734, I.1737, F.1738, V.1741, S.1742, I.1745 Ligands: PCW.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1737, A:F.1738, A:V.1741, A:I.1745 LPE.16: 3 residues within 4Å: Ligands: LPE.14, PCW.17, Y01.30 No protein-ligand interaction detected (PLIP) LPE.18: 9 residues within 4Å: Chain A: L.1295, L.1298, V.1311, Y.1658, F.1661, F.1738, Y.1739, I.1746 Ligands: LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1311 pi-Cation interactions: A:F.1661 LPE.19: 10 residues within 4Å: Chain A: N.1256, A.1257, W.1258, L.1261, L.1292, L.1295, V.1311, N.1312, I.1315 Ligands: LPE.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1292, A:L.1295 LPE.23: 7 residues within 4Å: Chain A: Q.1478, Y.1481, L.1641, F.1645, G.1648, L.1649 Ligands: P0T.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1649 Salt bridges: A:E.1477 LPE.24: 7 residues within 4Å: Chain A: T.319, D.320, K.376, M.379, L.1651, M.1655 Ligands: P0T.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1651 LPE.25: 6 residues within 4Å: Chain A: G.1207, A.1210, F.1211, F.1304, F.1656, F.1684 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1304, A:F.1656 Hydrogen bonds: A:A.1210 LPE.26: 7 residues within 4Å: Chain A: V.253, F.254, S.257, S.348, M.1533, A.1627 Ligands: PCW.20 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.253 LPE.27: 6 residues within 4Å: Chain A: W.1178, W.1179, R.1182, Y.1250 Ligands: P5S.8, LPE.28 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1182 LPE.28: 3 residues within 4Å: Chain A: K.1251 Ligands: P5S.8, LPE.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.1251 LPE.34: 5 residues within 4Å: Chain B: V.175, M.178, I.179, Y.182, K.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.178 LPE.35: 6 residues within 4Å: Chain A: F.1194, F.1197 Chain B: W.173, L.174, E.177, C.181 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.177

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

PCW.17: 14 residues within 4Å: Chain A: C.1328, L.1329, W.1332, N.1391, G.1393, L.1394, L.1397, L.1400, I.1737, V.1741, I.1745 Ligands: LPE.15, LPE.16, Y01.30 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1332, A:L.1394, A:L.1397, A:L.1400, A:I.1737, A:V.1741, A:I.1745 PCW.20: 12 residues within 4Å: Chain A: Y.339, G.340, Y.341, S.348, W.349, F.351, F.355, Q.941, A.942, L.945, M.949 Ligands: LPE.26 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.349, A:F.351, A:F.355, A:L.945, A:L.945, A:M.949 Hydrogen bonds: A:S.348, A:Q.941 PCW.22: 7 residues within 4Å: Chain A: L.1488, Q.1494, G.1577, F.1581, V.1584, L.1614 Ligands: P5S.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1581, A:V.1584, A:L.1614 Hydrogen bonds: A:G.1577 PCW.29: 3 residues within 4Å: Chain A: F.1574, V.1584, I.1587 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1584, A:I.1587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Cannabidiol inhibits Na v channels through two distinct binding sites. Nat Commun (2023)

Release Date

2023-07-05

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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