SMTL ID : 7xve.1

Human Nav1.7 mutant class-I

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

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.1386, D.1389, F.1393, S.1411 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1399, N.1400, S.1402, E.1403, K.1457 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.1409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1409 NAG.4: 1 residues within 4Å: Chain A: N.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.317 NAG.36: 2 residues within 4Å: Chain B: N.93, R.96 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.93, B:R.96 NAG.37: 2 residues within 4Å: Chain B: G.33, N.110 No protein-ligand interaction detected (PLIP) NAG.38: 3 residues within 4Å: Chain B: E.84, R.85, N.114 No protein-ligand interaction detected (PLIP) NAG.39: 2 residues within 4Å: Chain B: Y.124, N.135 No protein-ligand interaction detected (PLIP) NAG.40: 5 residues within 4Å: Chain C: S.64, N.66, Q.82, Y.128, R.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.64, C:N.66, C:R.137

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 12 residues within 4Å: Chain A: L.793, A.796, H.799, P.801, L.1363, L.1367, V.1426, G.1427, Y.1430 Ligands: LPE.7, LPE.10, PCW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.793, A:H.799, A:L.1363, A:L.1367, A:V.1426 Salt bridges: A:H.799

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 8 residues within 4Å: Chain A: I.262, P.263, G.898, G.901, N.902, M.904, L.905, F.908 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.262, A:L.905, A:F.908 CLR.23: 11 residues within 4Å: Chain A: F.1369, M.1372, L.1376, Y.1463, S.1464, L.1465, Y.1466, M.1467, I.1469, Y.1470, F.1473 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1376, A:L.1376, A:Y.1466, A:Y.1470, A:F.1473 CLR.24: 4 residues within 4Å: Chain A: F.1288, T.1289, A.1291, W.1294 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1291, A:W.1294, A:W.1294, A:W.1294 CLR.25: 6 residues within 4Å: Chain A: Y.1284, K.1285, F.1288, F.1297 Ligands: LPE.26, LPE.27 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.1284, A:Y.1284, A:K.1285, A:K.1285, A:F.1288, A:F.1288

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

LPE.7: 5 residues within 4Å: Chain A: M.797, H.799, F.806 Ligands: Y01.5, LPE.10 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.799 LPE.8: 9 residues within 4Å: Chain A: N.1766, P.1767, S.1768, I.1771, F.1772, V.1775, I.1779 Ligands: 1PW.9, PCW.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1772, A:V.1775, A:I.1779 Hydrogen bonds: A:S.1768, A:S.1768 LPE.10: 3 residues within 4Å: Ligands: Y01.5, LPE.7, PCW.11 No protein-ligand interaction detected (PLIP) LPE.12: 13 residues within 4Å: Chain A: S.1322, T.1325, L.1335, L.1684, V.1688, I.1691, Y.1692, F.1695, N.1699, V.1769, F.1772, Y.1773 Ligands: LPE.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1335, A:L.1684, A:V.1688, A:I.1691, A:Y.1692, A:Y.1773 Hydrogen bonds: A:N.1699, A:N.1699 LPE.13: 9 residues within 4Å: Chain A: A.1291, W.1292, L.1295, L.1329, V.1345, N.1346, I.1349, F.1695 Ligands: LPE.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1329, A:L.1329, A:F.1695 LPE.17: 9 residues within 4Å: Chain A: E.1339, T.1509, E.1511, Q.1512, Y.1515, L.1675, P.1676, L.1678, F.1679 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1675, A:F.1679 Hydrogen bonds: A:Q.1512 Salt bridges: A:E.1339 LPE.18: 3 residues within 4Å: Chain A: Y.1515, A.1518 Ligands: PCW.30 No protein-ligand interaction detected (PLIP) LPE.19: 9 residues within 4Å: Chain A: D.354, K.410, M.413, F.421, G.1682, G.1719, M.1722, I.1723 Ligands: LPE.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.421 Salt bridges: A:D.354 LPE.20: 9 residues within 4Å: Chain A: D.1247, Y.1249, R.1252, K.1253, T.1717, F.1718, G.1719 Ligands: LPE.19, LPE.21 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1718 Hydrogen bonds: A:K.1253 LPE.21: 10 residues within 4Å: Chain A: L.1237, S.1240, A.1244, F.1245, F.1338, L.1683, F.1686, L.1687, F.1690 Ligands: LPE.20 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1237, A:F.1338, A:L.1683, A:F.1686, A:F.1686, A:L.1687 pi-Cation interactions: A:F.1245 LPE.22: 13 residues within 4Å: Chain A: I.284, V.287, F.288, S.291, F.381, S.382, F.385, M.1567, L.1657, G.1660, A.1661, I.1664 Ligands: PCW.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.385, A:F.385 LPE.26: 9 residues within 4Å: Chain A: K.1210, W.1212, W.1213, R.1216, Y.1284 Ligands: CLR.25, LPE.27, LPE.28, LPE.29 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.1216 pi-Cation interactions: A:W.1213 LPE.27: 5 residues within 4Å: Chain A: Y.1284, K.1285 Ligands: CLR.25, LPE.26, LPE.28 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.1285 LPE.28: 13 residues within 4Å: Chain A: W.1212, W.1213, R.1216, Y.1220, W.1279, I.1280, A.1281, Y.1282, G.1283, Y.1284, K.1285 Ligands: LPE.26, LPE.27 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.1212, A:I.1280, A:Y.1284, A:Y.1284 Hydrogen bonds: A:R.1216 LPE.29: 2 residues within 4Å: Chain A: W.1212 Ligands: LPE.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.1212 LPE.32: 6 residues within 4Å: Chain A: N.188, Y.191, T.192, G.195, I.196, F.199 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.196, A:F.199 pi-Cation interactions: A:Y.191 LPE.34: 10 residues within 4Å: Chain A: K.1221, I.1222, H.1225, W.1227, F.1228, F.1231 Chain B: L.170, W.173, E.177, C.181 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.177 LPE.35: 6 residues within 4Å: Chain A: I.1211, I.1215 Chain B: V.175, M.178, I.179, Y.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.178

1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1PW.9: 12 residues within 4Å: Chain A: I.1352, I.1355, M.1356, T.1438, L.1483, F.1486, S.1731, I.1778, I.1779, F.1782 Ligands: LPE.8, PCW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.1438, A:L.1483, A:F.1486, A:F.1486, A:I.1779 Hydrogen bonds: A:S.1731

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

PCW.11: 16 residues within 4Å: Chain A: L.1359, C.1362, L.1363, W.1366, N.1425, G.1427, L.1428, L.1431, F.1486, I.1771, V.1775, I.1779 Ligands: Y01.5, LPE.8, 1PW.9, LPE.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1359, A:W.1366, A:W.1366, A:L.1428, A:L.1431, A:F.1486, A:I.1771, A:V.1775, A:I.1779 PCW.14: 15 residues within 4Å: Chain A: Y.373, G.374, Y.375, S.382, W.383, F.385, E.971, Q.975, A.976, L.979, I.980, M.983, M.984, F.987 Ligands: LPE.22 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.383, A:W.383, A:F.385, A:F.385, A:A.976, A:I.980, A:M.983, A:F.987 Hydrogen bonds: A:S.382, A:Q.975 PCW.15: 12 residues within 4Å: Chain A: F.288, F.293, G.1523, G.1611, W.1612, F.1615, R.1665, T.1666, L.1668, F.1669, A.1800 Ligands: PCW.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.288, A:F.293, A:F.1615, A:F.1615, A:L.1668, A:L.1668, A:L.1668 Salt bridges: A:R.1665 PCW.16: 12 residues within 4Å: Chain A: L.1522, T.1609, G.1611, I.1614, F.1615, V.1618, L.1648, I.1651, G.1652, M.1672 Ligands: PCW.15, PCW.30 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1615, A:V.1618, A:I.1651 Hydrogen bonds: A:G.1611 PCW.30: 6 residues within 4Å: Chain A: L.1522, V.1618, I.1622 Ligands: PCW.16, LPE.18, PCW.31 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1618, A:I.1622 PCW.31: 6 residues within 4Å: Chain A: F.1608, V.1618, I.1621, I.1622 Ligands: PCW.30, P5S.33 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.1608, A:V.1618, A:I.1621

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

P5S.33: 4 residues within 4Å: Chain A: L.1600, I.1601, H.1605 Ligands: PCW.31 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1600, A:I.1601 Hydrogen bonds: A:H.1605 Salt bridges: A:H.1605

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, G. et al., Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-08-10

Peptides

Sodium channel protein type 9 subunit alpha: A
Sodium channel subunit beta-1: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 9 subunit alpha

Sodium channel subunit beta-1

Sodium channel subunit beta-2

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