SMTL ID : 8xmm.1

Voltage-gated sodium channel Nav1.7 variant M9

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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.1395, D.1398, F.1402, S.1420, V.1423 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1408, N.1409, S.1411, E.1412 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.1418 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.326 NAG.23: 3 residues within 4Å: Chain B: V.91, N.93, F.107 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.25: 1 residues within 4Å: Chain B: N.114 No protein-ligand interaction detected (PLIP) NAG.26: 2 residues within 4Å: Chain B: Y.124, N.135 No protein-ligand interaction detected (PLIP)

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 7 residues within 4Å: Chain A: A.805, H.808, P.810, N.1434, V.1435, G.1436 Ligands: PCW.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.805, A:V.1435

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

LPE.6: 7 residues within 4Å: Chain A: N.1775, P.1776, S.1777, I.1780, V.1784, S.1785 Ligands: PCW.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1780, A:V.1784 Hydrogen bonds: A:N.1775, A:S.1777 LPE.8: 1 residues within 4Å: Ligands: PCW.9 No protein-ligand interaction detected (PLIP) LPE.10: 12 residues within 4Å: Chain A: S.1331, T.1334, L.1335, L.1357, I.1700, Y.1701, F.1704, N.1708, V.1778, F.1781, Y.1782 Ligands: LPE.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1357, A:I.1700, A:Y.1701, A:Y.1701, A:F.1704, A:F.1704 Hydrogen bonds: A:N.1708 LPE.11: 5 residues within 4Å: Chain A: A.1300, W.1301, N.1355, F.1704 Ligands: LPE.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1704 LPE.15: 4 residues within 4Å: Chain A: D.363, K.419, M.422, Y.1258 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.419 LPE.16: 10 residues within 4Å: Chain A: L.1246, S.1249, G.1250, A.1253, F.1254, D.1256, F.1695, L.1696, F.1699, F.1727 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1246, A:F.1695, A:L.1696 Salt bridges: A:D.1256 pi-Cation interactions: A:F.1254 LPE.17: 6 residues within 4Å: Chain A: W.1221, W.1222, R.1225, Y.1293 Ligands: LPE.18, LPE.19 No protein-ligand interaction detected (PLIP) LPE.18: 3 residues within 4Å: Chain A: K.1294 Ligands: LPE.17, LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.1294 Salt bridges: A:K.1294 LPE.19: 12 residues within 4Å: Chain A: W.1221, R.1225, Y.1229, W.1288, I.1289, A.1290, Y.1291, G.1292, Y.1293, T.1295 Ligands: LPE.17, LPE.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1221, A:I.1289, A:Y.1293, A:Y.1293 Hydrogen bonds: A:T.1295 Salt bridges: A:R.1225

1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1PW.7: 10 residues within 4Å: Chain A: I.1364, M.1365, L.1443, T.1447, F.1495, S.1740, I.1787, I.1788, F.1791 Ligands: PCW.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.1447, A:F.1495, A:F.1495, A:I.1788, A:F.1791

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

PCW.9: 14 residues within 4Å: Chain A: L.1368, C.1371, L.1372, W.1375, N.1434, G.1436, Y.1439, L.1440, L.1443, I.1780 Ligands: CLR.5, LPE.6, 1PW.7, LPE.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1368, A:L.1368, A:W.1375, A:W.1375, A:Y.1439, A:L.1443, A:I.1780 PCW.12: 12 residues within 4Å: Chain A: Y.382, Y.384, S.391, W.392, F.394, L.395, F.398, Q.984, L.988, I.989, M.992, M.993 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:L.395, A:F.398, A:L.988, A:I.989, A:M.992 Hydrogen bonds: A:S.391, A:Q.984 PCW.13: 14 residues within 4Å: Chain A: C.298, V.301, F.302, L.1531, G.1532, G.1620, W.1621, R.1674, T.1675, L.1677, F.1678, M.1681, A.1809 Ligands: PCW.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.301, A:F.302, A:W.1621, A:L.1677, A:L.1677 Salt bridges: A:R.1674 PCW.14: 12 residues within 4Å: Chain A: L.1531, K.1534, F.1617, T.1618, G.1620, I.1623, F.1624, I.1631, L.1657, M.1681 Ligands: PCW.13, PCW.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1624, A:I.1631 Hydrogen bonds: A:G.1620 Salt bridges: A:K.1534 PCW.20: 3 residues within 4Å: Chain A: I.1631 Ligands: PCW.14, PCW.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.1631 PCW.21: 8 residues within 4Å: Chain A: H.1614, F.1617, I.1623, V.1627, I.1630, I.1631 Ligands: PCW.20, P5S.22 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1617, A:I.1623, A:V.1627, A:I.1630, A:I.1630, A:I.1631 Salt bridges: A:H.1614

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

P5S.22: 6 residues within 4Å: Chain A: L.1609, I.1610, R.1613, H.1614, F.1626 Ligands: PCW.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1609, A:L.1609, A:I.1610 Salt bridges: A:R.1613, A:H.1614

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., Dissection of the structure-function relationship of Na v channels. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-03-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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