SMTL ID : 7wfw.1

Apo human Nav1.8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 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: K.1333, N.1336, F.1341, F.1342, W.1343 No protein-ligand interaction detected (PLIP)

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

NAG.2: 4 residues within 4Å: Chain A: N.815, N.816, K.818, N.819 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: N.312, C.325, L.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.312, A:C.325 NAG.4: 3 residues within 4Å: Chain A: N.1328, S.1330, D.1331 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: N.1312, T.1314, F.1341 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1341 Hydrogen bonds: A:N.1312

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: T.679, S.769, W.770, P.771, I.1290, L.1293 Ligands: LPE.19 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.679, A:W.770, A:I.1290, A:L.1293 CLR.13: 6 residues within 4Å: Chain A: K.728, I.731, F.732, F.758, L.761 Ligands: PCW.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.732, A:F.758, A:L.761, A:L.761 Hydrogen bonds: A:K.728 CLR.15: 3 residues within 4Å: Chain A: T.1215, A.1217, W.1220 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.1217, A:W.1220, A:W.1220, A:W.1220, A:W.1220, A:W.1220 CLR.20: 5 residues within 4Å: Chain A: S.341, A.343, I.1491, M.1494, V.1495 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.343, A:I.1491, A:I.1491, A:M.1494

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

PCW.7: 14 residues within 4Å: Chain A: F.260, F.382, L.1449, G.1450, W.1539, F.1542, R.1594, T.1595, L.1597, F.1598, L.1600, M.1601, L.1604 Ligands: PCW.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.260, A:F.382, A:W.1539, A:F.1542, A:F.1542, A:L.1597, A:L.1600, A:M.1601, A:L.1604 Salt bridges: A:R.1594 PCW.8: 15 residues within 4Å: Chain A: K.1452, T.1536, N.1537, G.1538, V.1541, F.1542, I.1545, L.1577, I.1580, G.1581, L.1584, M.1601 Ligands: PCW.7, LPE.10, LPE.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.1541, A:F.1542, A:F.1542, A:I.1580, A:L.1584 Salt bridges: A:K.1452 PCW.12: 7 residues within 4Å: Chain A: K.728, W.729, F.732, I.777, G.781, F.1404 Ligands: CLR.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.732, A:F.1404, A:F.1404 Hydrogen bonds: A:K.728

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

LPE.9: 8 residues within 4Å: Chain A: Q.1439, L.1604, P.1605, L.1607, F.1608, G.1611, M.1716 Ligands: LPE.10 No protein-ligand interaction detected (PLIP) LPE.10: 4 residues within 4Å: Chain A: Y.1442, M.1446 Ligands: PCW.8, LPE.9 No protein-ligand interaction detected (PLIP) LPE.11: 6 residues within 4Å: Chain A: I.372, Y.373, S.1568, T.1570, V.1574 Ligands: PCW.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.373 LPE.14: 5 residues within 4Å: Chain A: N.1216, A.1217, W.1218, L.1255, L.1258 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1255, A:L.1258 LPE.16: 8 residues within 4Å: Chain A: S.1166, G.1167, A.1170, F.1171, F.1615, L.1616, F.1619, F.1647 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1615, A:F.1615, A:L.1616, A:F.1619, A:F.1619 LPE.17: 2 residues within 4Å: Chain A: L.1289 Ligands: P5S.22 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1289 LPE.18: 1 residues within 4Å: Ligands: LPE.19 No protein-ligand interaction detected (PLIP) LPE.19: 6 residues within 4Å: Chain A: T.672, I.680, T.692, F.693 Ligands: CLR.6, LPE.18 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.672, A:I.680, A:I.680

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

P5S.21: 7 residues within 4Å: Chain A: W.344, F.350, K.863, S.864, L.867, L.871, T.872 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.344, A:F.350, A:L.871, A:L.871, A:T.872 Salt bridges: A:K.863, A:K.863 P5S.22: 13 residues within 4Å: Chain A: L.1285, C.1288, W.1292, N.1352, A.1354, L.1361, P.1695, A.1696, I.1699, T.1703, T.1704, I.1707 Ligands: LPE.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1285, A:W.1292, A:I.1699, A:I.1707 Hydrogen bonds: A:N.1352

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, X. et al., Structural basis for high-voltage activation and subtype-specific inhibition of human Na v 1.8. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-03

Peptides

Sodium channel protein type 10 subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 10 subunit alpha

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