SMTL ID : 8xmn.1

Voltage-gated sodium channel Nav1.7 variant M2

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: 4 residues within 4Å: Chain A: N.1409, S.1411, E.1412, K.1466 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: N.1395, T.1397, D.1398, F.1402, S.1420 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1418 NAG.4: 1 residues within 4Å: Chain A: N.326 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: N.93, F.107 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain B: G.33, M.34, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.15: 2 residues within 4Å: Chain B: E.84, N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114 NAG.16: 2 residues within 4Å: Chain B: L.126, N.135 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.126

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

LPE.5: 5 residues within 4Å: Chain A: A.805, H.808, L.1372, Y.1439 Ligands: PCW.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1372 Salt bridges: A:H.808 pi-Cation interactions: A:H.808 LPE.6: 6 residues within 4Å: Chain A: N.1775, P.1776, S.1777, I.1780, F.1781 Ligands: PCW.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1780, A:F.1781 Hydrogen bonds: A:N.1775, A:N.1775 LPE.8: 11 residues within 4Å: Chain A: S.1331, T.1334, L.1335, V.1697, Y.1701, F.1704, N.1708, V.1778, F.1781, Y.1782 Ligands: LPE.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.1697, A:Y.1701, A:F.1704, A:F.1781, A:F.1781, A:Y.1782 Hydrogen bonds: A:N.1708, A:N.1708 LPE.9: 5 residues within 4Å: Chain A: A.1300, W.1301, N.1355, I.1358 Ligands: LPE.8 No protein-ligand interaction detected (PLIP) LPE.12: 10 residues within 4Å: Chain A: S.1249, G.1250, A.1253, F.1254, D.1256, K.1262, L.1692, F.1695, F.1699, F.1727 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1692, A:F.1695, A:F.1695, A:F.1699 Salt bridges: A:D.1256

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

PCW.7: 9 residues within 4Å: Chain A: L.1368, L.1372, N.1434, G.1436, L.1437, Y.1439, L.1443 Ligands: LPE.5, LPE.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1368, A:L.1372, A:L.1437, A:Y.1439, A:L.1443 Hydrogen bonds: A:N.1434 PCW.10: 13 residues within 4Å: Chain A: Y.382, Y.384, S.391, W.392, F.394, F.398, E.980, Q.984, A.985, L.988, I.989, M.992, M.993 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.398, A:A.985, A:L.988, A:I.989, A:M.992 Hydrogen bonds: A:S.391, A:W.392, A:Q.984 Salt bridges: A:E.980 PCW.11: 10 residues within 4Å: Chain A: L.1531, T.1618, G.1620, I.1623, F.1624, V.1627, I.1631, L.1657, L.1664, M.1681 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1624, A:F.1624, A:V.1627, A:I.1631, A:L.1664 Hydrogen bonds: A:G.1620

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
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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