SMTL ID : 9dbm.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

5 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: 5 residues within 4Å: Chain A: N.319, N.357, C.370, L.371, 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.3: 7 residues within 4Å: Chain A: N.1357, T.1359, S.1364, P.1367, I.1370, T.1383, S.1385 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: 8 residues within 4Å: Chain A: C.1377, K.1378, N.1381, F.1386, F.1387, W.1388, P.1720, N.1726 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1726

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 11 residues within 4Å: Chain A: V.721, T.724, I.725, L.811, S.814, W.815, P.816, N.1328, I.1335, L.1338 Ligands: LPE.16 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.721, A:T.724, A:I.725, A:I.725, A:L.811, A:W.815, A:W.815, A:W.815, A:W.815, A:I.1335, A:L.1338 Hydrogen bonds: A:N.1328 CLR.7: 8 residues within 4Å: Chain A: K.773, I.776, F.777, I.780, V.799, F.803, L.806 Ligands: PCW.13 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.776, A:F.777, A:I.780, A:V.799, A:F.803, A:F.803, A:L.806, A:L.806 Hydrogen bonds: A:K.773 CLR.8: 5 residues within 4Å: Chain A: F.1259, W.1265, F.1268, L.1269, N.1272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.1259, A:W.1265, A:W.1265, A:W.1265, A:W.1265, A:W.1265, A:F.1268, A:L.1269, A:N.1272 CLR.9: 7 residues within 4Å: Chain A: F.387, A.388, I.1536, M.1539, V.1540, E.1541, T.1542 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.387, A:I.1536, A:T.1542 CLR.21: 15 residues within 4Å: Chain A: L.438, T.442, E.446, F.930, I.931, L.934, L.935, L.1455, V.1459, V.1759, Y.1762, I.1763, I.1766, F.1770 Ligands: LPE.11 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.438, A:T.442, A:I.931, A:L.934, A:L.935, A:L.1455, A:V.1459, A:V.1459, A:V.1759, A:Y.1762, A:I.1763, A:I.1766, A:F.1770

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

PCW.10: 17 residues within 4Å: Chain A: F.305, L.424, L.428, L.1494, K.1497, K.1498, Q.1500, G.1583, W.1584, V.1586, F.1587, R.1639, L.1642, L.1645, M.1646, L.1649 Ligands: LPE.12 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.305, A:L.428, A:W.1584, A:W.1584, A:L.1642, A:L.1645, A:M.1646, A:L.1649 Hydrogen bonds: A:R.1639 PCW.13: 12 residues within 4Å: Chain A: K.773, W.774, F.777, F.809, I.822, I.825, G.826, F.1336, F.1340, I.1445, F.1449 Ligands: CLR.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.777, A:F.777, A:F.809, A:F.809, A:F.809, A:I.822, A:I.825, A:F.1336, A:F.1340, A:F.1340, A:I.1445, A:F.1449, A:F.1449 Salt bridges: A:K.773 PCW.14: 10 residues within 4Å: Chain A: M.1343, L.1347, D.1435, N.1436, V.1437, Y.1438, M.1439, L.1441, Y.1442, I.1445 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1347, A:Y.1438, A:Y.1438, A:L.1441, A:Y.1442, A:I.1445 Hydrogen bonds: A:N.1436, A:Y.1438, A:M.1439

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

LPE.11: 12 residues within 4Å: Chain A: V.926, L.1406, A.1409, T.1410, F.1411, I.1447, G.1451, F.1452, L.1455, I.1752, F.1755 Ligands: CLR.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.926, A:F.1411, A:I.1447 LPE.12: 12 residues within 4Å: Chain A: V.308, L.312, I.417, Y.418, I.420, F.421, L.424, S.1613, T.1615, L.1616, V.1619 Ligands: PCW.10 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.308, A:L.312, A:I.420, A:L.424 LPE.15: 12 residues within 4Å: Chain A: T.1260, N.1261, A.1262, W.1263, L.1266, R.1313, V.1316, D.1317, L.1319, V.1320, V.1662, I.1753 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.1262, A:A.1262, A:W.1263, A:W.1263, A:L.1266, A:L.1266, A:V.1316, A:L.1319, A:V.1320, A:V.1320, A:V.1662, A:I.1753 Hydrogen bonds: A:A.1262, A:W.1263, A:R.1313, A:D.1317 LPE.16: 9 residues within 4Å: Chain A: A.728, E.730, H.731, G.733, L.1338, N.1397, V.1398 Ligands: CLR.6, LPE.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.728, A:L.1338, A:V.1398 Hydrogen bonds: A:N.1397 Salt bridges: A:H.731 LPE.17: 9 residues within 4Å: Chain A: I.725, M.729, H.731, G.733, M.734, S.735, F.738 Ligands: LPE.16, LPE.18 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.725 LPE.18: 8 residues within 4Å: Chain A: I.725, F.726, M.729, S.735, T.737, F.738, M.741 Ligands: LPE.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.725, A:I.725, A:F.726 Hydrogen bonds: A:T.737

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

P5S.19: 16 residues within 4Å: Chain A: L.1330, L.1334, W.1337, A.1399, Y.1402, L.1403, L.1406, F.1458, P.1740, A.1741, I.1744, I.1745, T.1748, T.1749, I.1752, I.1753 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.1330, A:L.1334, A:W.1337, A:L.1406, A:F.1458, A:T.1748, A:I.1752, A:I.1752, A:I.1752, A:I.1753 P5S.20: 12 residues within 4Å: Chain A: I.299, L.302, A.388, W.389, F.391, L.392, F.395, K.908, S.909, L.912, I.913, L.916 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.299, A:L.302, A:W.389, A:W.389, A:F.391, A:L.392, A:L.392, A:K.908, A:L.912, A:L.912, A:L.912, A:L.916, A:L.916 Salt bridges: A:K.908, 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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