SMTL ID : 7wfr.1

Human Nav1.8 with A-803467, class III

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: C.1332, 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.816, A:E.859 NAG.4: 4 residues within 4Å: Chain A: N.274, N.312, C.325, L.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.312, A:C.325 NAG.5: 3 residues within 4Å: Chain A: N.1312, T.1314, F.1341 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1341 Hydrogen bonds: A:N.1312

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

95T.6: 15 residues within 4Å: Chain A: Q.355, I.381, F.386, L.1614, T.1658, T.1659, S.1660, I.1706, F.1710, I.1712, M.1713, M.1716, Y.1717 Ligands: PCW.8, PCW.15 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1710, A:F.1710, A:M.1713 Hydrogen bonds: A:Q.355, A:Y.1717, A:Y.1717 pi-Stacking: A:F.386

5 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 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:W.770, A:L.1286, A:I.1290 CLR.19: 6 residues within 4Å: Chain A: K.728, I.735, F.758, L.761 Ligands: PCW.18, PCW.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.758, A:L.761 Hydrogen bonds: A:K.728 CLR.23: 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.29: 4 residues within 4Å: Chain A: S.341, M.1494, V.1495, T.1497 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1495, A:T.1497 CLR.30: 10 residues within 4Å: Chain A: L.393, F.885, L.889, V.1414, I.1418, F.1710, Y.1717, I.1718, I.1721 Ligands: PCW.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.393, A:F.885, A:L.889, A:I.1418, A:Y.1717, A:Y.1717

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

PCW.8: 17 residues within 4Å: Chain A: V.378, L.379, F.382, L.1449, G.1450, W.1539, I.1587, R.1594, T.1595, L.1597, F.1598, L.1600, M.1601, L.1604 Ligands: 95T.6, PCW.9, LPE.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.379, A:F.382, A:F.382, A:F.382, A:W.1539, A:W.1539, A:I.1587, A:M.1601, A:L.1604, A:L.1604 Salt bridges: A:R.1594 PCW.9: 9 residues within 4Å: Chain A: T.1536, N.1537, G.1538, I.1545, L.1577, M.1601 Ligands: PCW.8, LPE.11, LPE.17 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1545 Hydrogen bonds: A:G.1538 PCW.15: 13 residues within 4Å: Chain A: M.353, T.354, L.846, C.847, G.848, N.878, L.1361, T.1365, L.1410, F.1710 Ligands: 95T.6, LPE.16, CLR.30 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1361, A:T.1365, A:L.1410, A:L.1410, A:F.1710 Hydrogen bonds: A:N.878 PCW.18: 11 residues within 4Å: Chain A: K.728, W.729, F.764, I.777, I.780, G.781, I.1400, F.1404 Ligands: LPE.16, CLR.19, PCW.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.764, A:I.780, A:I.1400 Salt bridges: A:K.728 PCW.20: 6 residues within 4Å: Chain A: V.754, Y.1393, M.1394, Y.1397 Ligands: PCW.18, CLR.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.754, A:V.754, A:Y.1397 PCW.21: 7 residues within 4Å: Chain A: S.1694, P.1695, A.1696, V.1697, I.1700 Ligands: LPE.22, P5S.31 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1697, A:I.1700 Hydrogen bonds: A:A.1696 PCW.28: 8 residues within 4Å: Chain A: I.1491, T.1492, V.1495, D.1499, Q.1500, S.1501, K.1504, I.1507 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.1491, A:T.1492, A:V.1495 Salt bridges: A:K.1504

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

LPE.10: 7 residues within 4Å: Chain A: L.1604, P.1605, L.1607, F.1608, M.1716 Ligands: PCW.8, LPE.11 No protein-ligand interaction detected (PLIP) LPE.11: 3 residues within 4Å: Chain A: Y.1442 Ligands: PCW.9, LPE.10 No protein-ligand interaction detected (PLIP) LPE.12: 4 residues within 4Å: Chain A: I.251, A.1589, K.1591 Ligands: LPE.13 No protein-ligand interaction detected (PLIP) LPE.13: 6 residues within 4Å: Chain A: A.247, T.250, I.251, I.254 Ligands: LPE.12, LPE.14 No protein-ligand interaction detected (PLIP) LPE.14: 6 residues within 4Å: Chain A: V.243, K.244, L.246, A.247, T.250 Ligands: LPE.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.243, A:L.246 Salt bridges: A:K.244 LPE.16: 14 residues within 4Å: Chain A: I.780, S.783, V.784, T.791, L.794, F.843, L.846, V.881, L.884, I.1403, F.1407, F.1408 Ligands: PCW.15, PCW.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.784, A:T.791, A:F.1408 Hydrogen bonds: A:I.1403 LPE.17: 8 residues within 4Å: Chain A: Y.373, F.376, L.379, S.1568, T.1570, L.1571, V.1574 Ligands: PCW.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.379 Hydrogen bonds: A:T.1570 LPE.22: 7 residues within 4Å: Chain A: N.1216, A.1217, W.1218, L.1255, L.1258, D.1272 Ligands: PCW.21 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.1218, A:W.1218, A:L.1255, A:L.1258 LPE.24: 7 residues within 4Å: Chain A: G.1167, A.1170, F.1171, F.1615, L.1616, F.1619, F.1647 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1615, A:L.1616, A:F.1619 pi-Cation interactions: A:F.1171 LPE.25: 1 residues within 4Å: Ligands: P5S.31 No protein-ligand interaction detected (PLIP) LPE.26: 4 residues within 4Å: Chain A: I.680, M.684, F.693 Ligands: LPE.27 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.680 LPE.27: 5 residues within 4Å: Chain A: I.680, S.690, T.692, M.696 Ligands: LPE.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.680 Hydrogen bonds: A:T.692

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

P5S.31: 14 residues within 4Å: Chain A: C.1288, L.1289, W.1292, N.1352, A.1354, M.1355, L.1361, P.1695, A.1696, I.1699, T.1703, I.1707 Ligands: PCW.21, LPE.25 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1289, A:W.1292, A:W.1292, A:A.1354, A:I.1699, A:I.1699, 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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