SMTL ID : 9dbl.1

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

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: 3 residues within 4Å: Chain A: 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: 10 residues within 4Å: Chain A: C.1377, K.1378, N.1381, G.1384, F.1386, F.1387, W.1388, P.1720, N.1726, R.1734 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1726, A:R.1734, A:R.1734, 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, T.1383 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.1383

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 12 residues within 4Å: Chain A: L.438, T.442, E.446, I.931, L.935, V.1459, I.1463, V.1759, Y.1762, I.1763, I.1766, F.1770 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.438, A:T.442, A:E.446, A:I.931, A:L.935, A:V.1459, A:V.1459, A:V.1759, A:Y.1762, A:I.1763, A:I.1766, A:F.1770 CLR.7: 8 residues within 4Å: Chain A: V.721, T.724, V.808, L.811, S.814, W.815, P.816, I.1335 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.721, A:T.724, A:V.808, A:L.811, A:W.815, A:W.815 CLR.8: 6 residues within 4Å: Chain A: K.773, I.776, I.780, F.803, L.806 Ligands: PCW.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.773, A:I.776, A:I.780, A:L.806 CLR.9: 5 residues within 4Å: Chain A: T.1260, A.1262, W.1265, L.1269 Ligands: LPE.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.1262, A:W.1265, A:W.1265, A:W.1265, A:L.1269 Hydrogen bonds: A:T.1260 CLR.10: 7 residues within 4Å: Chain A: S.386, F.387, I.1536, M.1539, V.1540, E.1541, T.1542 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.387, A:F.387, A:I.1536 Hydrogen bonds: A:F.387, A:E.1541

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

PCW.11: 20 residues within 4Å: Chain A: L.1494, K.1498, Q.1500, T.1581, N.1582, G.1583, W.1584, V.1586, F.1587, I.1590, L.1594, A.1623, I.1625, G.1626, L.1629, R.1639, L.1642, L.1645, M.1646, L.1649 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.1584, A:V.1586, A:F.1587, A:F.1587, A:F.1587, A:I.1590, A:I.1590, A:L.1594, A:I.1625, A:L.1629, A:L.1642, A:L.1642, A:L.1645, A:L.1645, A:L.1649 PCW.14: 11 residues within 4Å: Chain A: K.773, W.774, F.777, F.809, I.822, I.825, G.826, V.829, I.1445, F.1449 Ligands: CLR.8 13 PLIP interactions: 13 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:I.1445, A:F.1449, A:F.1449 Hydrogen bonds: A:W.774 PCW.15: 6 residues within 4Å: Chain A: V.799, M.1343, L.1347, Y.1438, L.1441, Y.1442 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.799, A:V.799, A:L.1347, A:L.1441, A:L.1441, A:Y.1442

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

LPE.12: 12 residues within 4Å: Chain A: L.839, L.1406, A.1409, T.1410, F.1411, I.1447, I.1448, G.1451, L.1455, I.1751, I.1752, F.1755 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.839, A:I.1448 LPE.13: 16 residues within 4Å: Chain A: V.308, L.312, G.358, S.359, D.360, S.361, S.414, G.415, I.417, Y.418, I.420, F.421, L.424, T.1615, L.1616, V.1619 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.308, A:L.312, A:I.420, A:F.421, A:L.424 Hydrogen bonds: A:T.1615 LPE.16: 13 residues within 4Å: Chain A: K.1257, T.1260, N.1261, A.1262, W.1263, L.1266, I.1270, L.1300, L.1303, L.1306, V.1316, D.1317 Ligands: CLR.9 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.1262, A:W.1263, A:L.1266, A:L.1266, A:L.1266, A:I.1270, A:L.1300, A:L.1303, A:L.1306, A:V.1316 Hydrogen bonds: A:N.1261, A:A.1262 Salt bridges: A:K.1257 LPE.17: 10 residues within 4Å: Chain A: D.360, K.416, I.417, M.419, Y.1220, D.1685, T.1691, A.1693, N.1694, M.1696 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1693, A:M.1696 Salt bridges: A:K.416, A:D.1685 LPE.18: 8 residues within 4Å: Chain A: A.728, M.729, H.731, G.733, L.1338, N.1397, V.1398 Ligands: LPE.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.728, A:L.1338, A:V.1398 LPE.19: 7 residues within 4Å: Chain A: I.725, M.729, H.731, S.735, F.738 Ligands: LPE.18, LPE.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.725 Salt bridges: A:H.731 LPE.20: 8 residues within 4Å: Chain A: I.725, F.726, M.729, S.735, T.737, F.738, M.741 Ligands: LPE.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.725

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

P5S.21: 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, Y.1666, A.1741, I.1744, I.1745, F.1746, T.1748, T.1749 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.1330, A:L.1334, A:W.1337, A:L.1406, A:L.1406, A:I.1744, A:I.1745, A:I.1745, A:F.1746, A:T.1748 Hydrogen bonds: A:N.1397, A:A.1741 P5S.22: 14 residues within 4Å: Chain A: N.380, Y.381, W.389, F.391, L.392, F.395, M.903, 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:W.389, A:F.391, A:F.395, A:F.395, A:K.908, A:K.908, A:L.912, A:L.912, A:L.916, A:L.916, A:V.920, A:V.920 Hydrogen bonds: A:N.380 Salt bridges: A:K.908, 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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