SMTL ID : 7wel.1

Human Nav1.8 with A-803467, class II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

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: 3 residues within 4Å: Chain A: N.1328, S.1330, D.1331 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: K.1333, N.1336, G.1339, F.1341, F.1342, W.1343 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.819, E.859, V.860 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.819, A:E.859 NAG.4: 2 residues within 4Å: Chain A: N.312, C.325 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.312, A:C.325, A:C.325 NAG.5: 5 residues within 4Å: Chain A: N.1312, T.1314, S.1319, T.1338, S.1340 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:S.1319 Hydrogen bonds: A:S.1340

1 x 95T: 5-(4-chlorophenyl)-~{N}-(3,5-dimethoxyphenyl)furan-2-carboxamide(Non-covalent)

95T.6: 14 residues within 4Å: Chain A: Q.355, F.382, S.385, L.1614, F.1655, T.1658, T.1659, S.1660, I.1706, S.1709, F.1710, M.1713, M.1716 Ligands: PCW.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.382, A:T.1659, A:F.1710, A:M.1713 Hydrogen bonds: A:Q.355, A:Q.355

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 13 residues within 4Å: Chain A: L.393, T.397, E.401, F.885, I.886, L.890, V.1414, I.1418, M.1713, V.1714, Y.1717, I.1721, F.1725 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.393, A:T.397, A:F.885, A:I.886, A:V.1414, A:I.1418, A:V.1714, A:Y.1717, A:Y.1717, A:I.1721, A:F.1725 CLR.8: 5 residues within 4Å: Chain A: T.679, S.769, W.770, L.1286, I.1290 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.679, A:W.770, A:I.1290 CLR.20: 6 residues within 4Å: Chain A: K.728, I.735, F.758, L.761 Ligands: PCW.19, PCW.21 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.728, A:I.735, A:F.758, A:F.758, A:L.761 CLR.23: 2 residues within 4Å: Chain A: T.1215, W.1220 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.1215 CLR.30: 7 residues within 4Å: Chain A: F.342, A.343, I.1491, M.1494, V.1495, T.1497 Ligands: PCW.29 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.342, A:I.1491, A:I.1491, A:M.1494, A:V.1495

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

PCW.9: 17 residues within 4Å: Chain A: C.256, F.260, L.379, G.1450, W.1539, F.1542, I.1587, R.1594, T.1595, L.1597, F.1598, M.1601, L.1604, V.1727 Ligands: 95T.6, PCW.10, LPE.11 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.260, A:L.379, A:W.1539, A:W.1539, A:F.1542, A:I.1587, A:L.1597, A:L.1604, A:L.1604 Salt bridges: A:R.1594 PCW.10: 12 residues within 4Å: Chain A: L.1449, K.1452, T.1536, G.1538, F.1542, I.1545, L.1577, G.1581, L.1584 Ligands: PCW.9, LPE.12, PCW.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1545, A:L.1584 Hydrogen bonds: A:G.1538 Salt bridges: A:K.1452 PCW.13: 1 residues within 4Å: Ligands: PCW.10 No protein-ligand interaction detected (PLIP) PCW.14: 7 residues within 4Å: Chain A: R.1475, Q.1476, A.1477, I.1480, T.1481, V.1484, F.1514 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.1475, A:Q.1476, A:V.1484, A:F.1514 Hydrogen bonds: A:T.1481 PCW.19: 9 residues within 4Å: Chain A: K.728, W.729, F.732, F.764, I.777, G.781, F.1404 Ligands: CLR.20, PCW.21 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.729, A:F.764, A:F.764, A:F.1404, A:F.1404, A:F.1404, A:F.1404 Salt bridges: A:K.727 PCW.21: 9 residues within 4Å: Chain A: V.754, F.758, M.1298, Y.1393, L.1396, Y.1397, I.1400 Ligands: PCW.19, CLR.20 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.754, A:V.754, A:F.758, A:L.1396, A:Y.1397, A:I.1400 PCW.29: 7 residues within 4Å: Chain A: T.1492, V.1495, D.1499, Q.1500, S.1501, K.1504 Ligands: CLR.30 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.1495, A:K.1504 Salt bridges: A:K.1504, A:K.1504

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

LPE.11: 7 residues within 4Å: Chain A: F.382, Y.1442, P.1605, L.1607, F.1608, G.1611 Ligands: PCW.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.382, A:F.382 LPE.12: 2 residues within 4Å: Chain A: L.1449 Ligands: PCW.10 No protein-ligand interaction detected (PLIP) LPE.15: 4 residues within 4Å: Chain A: I.254, K.1591, G.1592 Ligands: LPE.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.254 LPE.16: 6 residues within 4Å: Chain A: A.247, T.250, I.251 Ligands: LPE.15, LPE.17, P5S.31 No protein-ligand interaction detected (PLIP) LPE.17: 7 residues within 4Å: Chain A: V.243, K.244, L.246, A.247, T.250, V.875 Ligands: LPE.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.246, A:V.875 LPE.18: 8 residues within 4Å: Chain A: I.372, Y.373, I.375, F.376, S.1568, T.1570, L.1571, V.1574 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.375, A:F.376 LPE.22: 4 residues within 4Å: Chain A: N.1216, A.1217, W.1218, L.1255 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1255 LPE.24: 7 residues within 4Å: Chain A: S.1166, G.1167, A.1170, F.1171, D.1173, L.1616, F.1647 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1616 LPE.25: 3 residues within 4Å: Chain A: Y.1357 Ligands: LPE.28, P5S.32 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1357 LPE.26: 4 residues within 4Å: Chain A: M.684, F.693 Ligands: LPE.27, LPE.28 No protein-ligand interaction detected (PLIP) LPE.27: 4 residues within 4Å: Chain A: I.680, S.690, T.692 Ligands: LPE.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.680 Hydrogen bonds: A:T.692 LPE.28: 2 residues within 4Å: Ligands: LPE.25, LPE.26 No protein-ligand interaction detected (PLIP)

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

P5S.31: 9 residues within 4Å: Chain A: Y.336, W.344, F.350, K.863, S.864, L.867, L.871, T.872 Ligands: LPE.16 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.350, A:L.871, A:L.871, A:T.872 Salt bridges: A:K.863, A:K.863 P5S.32: 14 residues within 4Å: Chain A: C.1288, W.1292, N.1352, A.1354, M.1355, L.1361, P.1695, A.1696, I.1699, I.1700, T.1703, T.1704, I.1707 Ligands: LPE.25 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.1292, A:W.1292, A:A.1354, A:A.1696, A:I.1699, A:I.1700, A:T.1704, 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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