SMTL ID : 8xmo.1

Voltage-gated sodium channel Nav1.7 variant M4

Coordinates

PDB Format

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: 4 residues within 4Å: Chain B: N.1395, T.1397, D.1398, F.1402 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: P.1408, N.1409, E.1412, K.1466 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 B: N.1418 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain B: N.326 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.326 NAG.17: 1 residues within 4Å: Chain C: N.93 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain C: F.54, Y.124, N.135, T.136, S.137 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain C: G.33, N.110 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.33 NAG.20: 3 residues within 4Å: Chain C: E.84, R.89, N.114 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.89, C:N.114

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

LPE.5: 4 residues within 4Å: Chain B: P.1776, S.1777, I.1780 Ligands: PCW.7 No protein-ligand interaction detected (PLIP) LPE.6: 1 residues within 4Å: Ligands: PCW.7 No protein-ligand interaction detected (PLIP) LPE.8: 11 residues within 4Å: Chain B: S.1331, L.1357, V.1697, I.1700, Y.1701, F.1704, N.1708, N.1775, V.1778, F.1781 Ligands: LPE.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.1357, B:V.1697, B:I.1700, B:Y.1701, B:F.1704 Hydrogen bonds: B:N.1708 LPE.9: 5 residues within 4Å: Chain B: A.1300, W.1301, L.1304, L.1341 Ligands: LPE.8 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.1304, B:L.1341 LPE.13: 5 residues within 4Å: Chain B: D.363, K.419, T.420, M.422, Y.1258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.363 Salt bridges: B:K.419 LPE.14: 9 residues within 4Å: Chain B: S.1249, G.1250, A.1253, F.1254, F.1347, L.1692, L.1696, F.1699, F.1727 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.1347, B:L.1692, B:L.1696, B:F.1699 pi-Cation interactions: B:F.1254 LPE.15: 2 residues within 4Å: Chain B: G.1292, K.1294 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.1293

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

PCW.7: 9 residues within 4Å: Chain B: L.1372, W.1375, N.1434, G.1436, L.1440, I.1780, V.1784 Ligands: LPE.5, LPE.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.1372, B:L.1372, B:L.1440, B:I.1780, B:V.1784 Hydrogen bonds: B:N.1434 PCW.10: 10 residues within 4Å: Chain B: Y.382, G.383, Y.384, S.391, W.392, F.394, Q.984, L.988, I.989, M.992 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.392, B:F.394, B:L.988, B:I.989, B:M.992 Hydrogen bonds: B:S.391 PCW.11: 12 residues within 4Å: Chain B: F.302, L.431, G.1620, W.1621, F.1624, V.1667, R.1674, T.1675, L.1677, F.1678, L.1680 Ligands: PCW.12 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.302, B:L.431, B:W.1621, B:F.1624, B:F.1624, B:V.1667, B:L.1677, B:L.1677, B:L.1680 Salt bridges: B:R.1674 pi-Cation interactions: B:F.1678 PCW.12: 9 residues within 4Å: Chain B: L.1531, T.1618, V.1619, G.1620, F.1624, I.1631, L.1657 Ligands: PCW.11, PCW.16 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.1624, B:I.1631, B:L.1657 Hydrogen bonds: B:G.1620 PCW.16: 1 residues within 4Å: Ligands: PCW.12 No protein-ligand interaction detected (PLIP)

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 subunit beta-2: A
Sodium channel protein type 9 subunit alpha: B
Sodium channel subunit beta-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel subunit beta-2

Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

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