SMTL ID : 7we4.1

Human Nav1.8 with A-803467, class I

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: 4 residues within 4Å: Chain A: N.1327, N.1328, S.1330, D.1331 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: K.1333, N.1336, 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.816, N.819, E.859 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.819, A:E.859 NAG.4: 3 residues within 4Å: Chain A: N.312, C.325, L.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.312, A:C.325, A:C.325 NAG.5: 3 residues within 4Å: Chain A: N.1312, T.1314, F.1341 No protein-ligand interaction detected (PLIP)

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

95T.6: 10 residues within 4Å: Chain A: Q.355, T.1365, L.1614, T.1658, T.1659, S.1660, I.1706, S.1709, F.1710, M.1713 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1710, A:M.1713 Hydrogen bonds: A:Q.355

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 5 residues within 4Å: Chain A: T.679, L.766, S.769, W.770, I.1290 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.679, A:L.766, A:W.770, A:W.770, A:I.1290 CLR.18: 3 residues within 4Å: Chain A: T.1215, A.1217, W.1220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.1217, A:W.1220, A:W.1220 CLR.23: 4 residues within 4Å: Chain A: S.341, F.342, M.1494, V.1495 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.342, A:V.1495 CLR.27: 13 residues within 4Å: Chain A: L.393, T.397, E.401, I.886, L.889, V.1414, I.1418, M.1713, V.1714, Y.1717, I.1718, I.1721, F.1725 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.393, A:T.397, A:I.886, A:L.889, A:V.1414, A:I.1418, A:V.1714, A:Y.1717, A:Y.1717, A:I.1718, A:F.1725

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

PCW.8: 15 residues within 4Å: Chain A: F.260, F.382, G.1450, G.1538, W.1539, F.1542, I.1587, R.1594, T.1595, L.1597, F.1598, M.1601, L.1604, V.1727 Ligands: PCW.9 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.260, A:F.382, A:W.1539, A:W.1539, A:F.1542, A:I.1587, A:L.1604 Salt bridges: A:R.1594 PCW.9: 11 residues within 4Å: Chain A: K.1452, T.1536, N.1537, G.1538, F.1542, L.1577, M.1601 Ligands: PCW.8, LPE.11, PCW.12, LPE.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1542 Hydrogen bonds: A:G.1538 Salt bridges: A:K.1452 PCW.12: 1 residues within 4Å: Ligands: PCW.9 No protein-ligand interaction detected (PLIP) PCW.15: 11 residues within 4Å: Chain A: K.728, W.729, F.732, F.764, I.777, G.781, F.1295, I.1400, F.1404 Ligands: LPE.13, PCW.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.729, A:F.764, A:F.1295, A:I.1400, A:F.1404, A:F.1404 Salt bridges: A:K.728 PCW.16: 7 residues within 4Å: Chain A: V.754, M.1298, Y.1393, M.1394, Y.1397, I.1400 Ligands: PCW.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.754, A:Y.1397, A:I.1400

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

LPE.10: 7 residues within 4Å: Chain A: Q.1439, Y.1442, P.1605, L.1607, F.1608, G.1611, M.1716 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.1439 LPE.11: 2 residues within 4Å: Chain A: L.1449 Ligands: PCW.9 No protein-ligand interaction detected (PLIP) LPE.13: 16 residues within 4Å: Chain A: I.780, S.783, V.784, T.791, L.794, F.843, L.846, V.881, L.884, F.1366, I.1402, I.1403, F.1404, F.1407, F.1408 Ligands: PCW.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.784, A:T.791, A:I.1403, A:F.1404, A:F.1404, A:F.1408 Hydrogen bonds: A:I.1403 LPE.14: 9 residues within 4Å: Chain A: Y.373, F.376, L.379, F.1567, S.1568, T.1570, L.1571, V.1574 Ligands: PCW.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.376, A:L.379 LPE.17: 3 residues within 4Å: Chain A: N.1216, A.1217, W.1218 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1217, A:W.1218, A:W.1218 Hydrogen bonds: A:A.1217 LPE.19: 8 residues within 4Å: Chain A: S.1166, G.1167, A.1170, F.1171, F.1615, L.1616, F.1619, F.1647 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1616, A:F.1619 LPE.20: 1 residues within 4Å: Ligands: P5S.24 No protein-ligand interaction detected (PLIP) LPE.21: 2 residues within 4Å: Chain A: M.684 Ligands: LPE.22 No protein-ligand interaction detected (PLIP) LPE.22: 5 residues within 4Å: Chain A: I.680, S.690, T.692, M.696 Ligands: LPE.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.680 Hydrogen bonds: A:T.692

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

P5S.24: 16 residues within 4Å: Chain A: L.1285, C.1288, L.1289, 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.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1285, A:L.1289, A:W.1292, A:L.1361, A:I.1699, A:I.1700, A:T.1704, A:I.1707 Hydrogen bonds: A:N.1352 P5S.25: 5 residues within 4Å: Chain A: F.1468, I.1472, R.1475, F.1478, M.1525 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1468, A:I.1472, A:F.1478 Hydrogen bonds: A:R.1475 Salt bridges: A:R.1475 P5S.26: 8 residues within 4Å: Chain A: Y.336, W.344, F.350, K.863, S.864, L.867, L.871, T.872 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.350, A:L.867, A:L.871, A:L.871, A:L.871, A:T.872 Salt bridges: A:K.863, A:K.863

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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