SMTL ID : 9dbk.1

Full-length apo human voltage-gated sodium channel 1.8 (NaV1.8)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: N.319, N.357, C.370, K.372 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.861, N.864, E.904, V.905 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain A: N.1372, N.1373, S.1375, D.1376 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: C.1377, K.1378, N.1381, G.1384, F.1386, F.1387, P.1720 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.1720

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.3: 5 residues within 4Å: Chain A: N.1357, T.1359, P.1367, I.1370, S.1385 No protein-ligand interaction detected (PLIP)

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 7 residues within 4Å: Chain A: V.721, T.724, L.811, S.814, W.815, I.1335 Ligands: LPE.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.721, A:T.724, A:L.811, A:W.815, A:W.815, A:W.815 CLR.7: 9 residues within 4Å: Chain A: K.773, F.777, I.780, L.797, V.799, F.803, L.806 Ligands: PCW.13, PCW.14 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.777, A:F.777, A:I.780, A:L.797, A:V.799, A:F.803, A:F.803 Hydrogen bonds: A:K.773 CLR.8: 5 residues within 4Å: Chain A: T.1260, A.1262, W.1265, L.1269 Ligands: LPE.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.1262, A:W.1265, A:W.1265, A:W.1265, A:W.1265, A:W.1265, A:L.1269 CLR.9: 6 residues within 4Å: Chain A: S.386, F.387, A.388, I.1536, M.1539, T.1542 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.387, A:A.388, A:I.1536, A:I.1536 Hydrogen bonds: A:S.386 CLR.22: 13 residues within 4Å: Chain A: L.438, F.930, I.931, L.934, L.935, V.1459, I.1463, F.1466, Y.1762, I.1763, I.1766, L.1767, F.1770 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.438, A:F.930, A:I.931, A:L.934, A:L.935, A:V.1459, A:I.1463, A:F.1466, A:Y.1762, A:I.1763, A:I.1766, A:L.1767, A:F.1770, A:F.1770

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

PCW.10: 19 residues within 4Å: Chain A: V.308, L.1494, K.1497, Q.1500, K.1501, T.1581, G.1583, W.1584, F.1587, I.1590, L.1594, L.1622, I.1625, G.1626, R.1639, L.1642, L.1645, M.1646 Ligands: LPE.12 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.308, A:W.1584, A:F.1587, A:F.1587, A:I.1590, A:L.1594, A:I.1625, A:I.1625, A:L.1642, A:L.1645 Hydrogen bonds: A:G.1583 Salt bridges: A:K.1497, A:R.1639 PCW.13: 14 residues within 4Å: Chain A: K.772, K.773, W.774, F.777, F.809, I.822, I.825, G.826, V.829, F.1336, I.1445, F.1449 Ligands: CLR.7, PCW.14 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.774, A:F.777, A:F.777, A:F.809, A:F.809, A:F.809, A:I.822, A:I.825, A:V.829, A:V.829, A:F.1336, A:I.1445, A:F.1449, A:F.1449, A:F.1449 Hydrogen bonds: A:K.773, A:W.774 PCW.14: 12 residues within 4Å: Chain A: V.799, M.1343, D.1435, N.1436, V.1437, Y.1438, M.1439, L.1441, Y.1442, I.1445 Ligands: CLR.7, PCW.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.799, A:Y.1438, A:L.1441, A:L.1441, A:I.1445, A:I.1445 Hydrogen bonds: A:V.1437, A:Y.1438

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

LPE.11: 15 residues within 4Å: Chain A: I.825, S.828, V.829, T.836, L.839, F.888, V.926, L.929, F.1411, I.1447, I.1448, F.1449, G.1451, F.1452, F.1453 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.825, A:T.836, A:F.1449, A:F.1449, A:F.1453 LPE.12: 12 residues within 4Å: Chain A: F.305, V.308, L.312, I.417, Y.418, F.421, L.424, S.1613, T.1615, L.1616, V.1619 Ligands: PCW.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.305, A:V.308, A:L.312, A:F.421, A:L.424 Hydrogen bonds: A:Y.418 LPE.15: 11 residues within 4Å: Chain A: T.1260, N.1261, A.1262, W.1263, L.1269, L.1300, L.1303, R.1313, D.1317, V.1320 Ligands: CLR.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.1262, A:W.1263, A:W.1263, A:L.1269, A:L.1300, A:L.1303 Hydrogen bonds: A:W.1263, A:R.1313 LPE.16: 7 residues within 4Å: Chain A: D.360, K.416, I.417, M.419, F.1660, A.1693, M.1696 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1660, A:F.1660 Salt bridges: A:D.360 LPE.17: 7 residues within 4Å: Chain A: A.728, M.729, H.731, G.733, L.1338, Y.1402 Ligands: LPE.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.728, A:L.1338 Hydrogen bonds: A:A.728 Salt bridges: A:H.731 LPE.18: 7 residues within 4Å: Chain A: I.725, M.729, H.731, F.738 Ligands: CLR.6, LPE.17, LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.725, A:I.725 LPE.19: 10 residues within 4Å: Chain A: L.718, V.722, I.725, F.726, M.729, S.735, T.737, F.738, M.741 Ligands: LPE.18 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.718, A:V.722, A:V.722, A:I.725, A:I.725, A:F.726

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

P5S.20: 17 residues within 4Å: Chain A: L.1330, C.1333, L.1334, W.1337, N.1397, A.1399, M.1400, Y.1402, L.1403, L.1406, P.1740, A.1741, I.1744, I.1745, T.1748, T.1749, I.1752 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.1330, A:L.1334, A:W.1337, A:Y.1402, A:L.1403, A:L.1406, A:A.1741, A:I.1744, A:I.1745, A:I.1745, A:I.1752, A:I.1752, A:I.1752 Hydrogen bonds: A:N.1397 P5S.21: 14 residues within 4Å: Chain A: N.380, Y.381, A.388, W.389, F.391, L.392, F.395, K.908, S.909, L.912, I.913, L.916, T.917, V.920 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.389, A:F.391, A:F.391, A:L.392, A:L.392, A:F.395, A:F.395, A:L.912, A:L.912, A:I.913, A:L.916, A:L.916, A:L.916, A:V.920 Hydrogen bonds: A:N.380 Salt bridges: A:K.908

Links

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Citation

Neumann, B. et al., Structural basis of inhibition of human Na V 1.8 by the tarantula venom peptide Protoxin-I. Nat Commun (2025)

Release Date

2025-02-19

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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