SMTL ID : 7xvf.1

Nav1.7 mutant class2

Coordinates

PDB Format Compare

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: 5 residues within 4Å: Chain A: N.1386, T.1388, D.1389, F.1393, S.1411 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1399, N.1400, 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 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain A: N.316, N.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.317 NAG.35: 4 residues within 4Å: Chain B: V.91, N.93, R.96, F.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.93, B:R.96 NAG.36: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.110 NAG.37: 1 residues within 4Å: Chain B: N.114 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.114 NAG.38: 1 residues within 4Å: Chain B: N.135 No protein-ligand interaction detected (PLIP) NAG.40: 5 residues within 4Å: Chain C: N.66, Q.82, R.84, Y.128, R.137 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.66, C:Q.82, C:R.137

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.5: 12 residues within 4Å: Chain A: A.796, M.797, H.799, P.801, L.1363, L.1367, N.1425, G.1427, Y.1430 Ligands: LPE.7, LPE.10, PCW.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.796, A:L.1367, A:L.1367 Hydrogen bonds: A:H.799 Salt bridges: A:H.799 Y01.23: 12 residues within 4Å: Chain A: F.871, F.1369, M.1372, Y.1463, S.1464, L.1465, Y.1466, M.1467, I.1469, Y.1470, F.1473 Ligands: Y01.24 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.871, A:F.1369, A:F.1369, A:I.1469, A:I.1469, A:F.1473, A:F.1473 Hydrogen bonds: A:Y.1466 Y01.24: 4 residues within 4Å: Chain A: E.1462, Y.1463, L.1465 Ligands: Y01.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.1463, A:L.1465 Y01.25: 3 residues within 4Å: Chain A: T.1289, W.1294, L.1298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.1294, A:W.1294, A:L.1298 Y01.26: 6 residues within 4Å: Chain A: W.1279, Y.1284, K.1285, F.1288, F.1297 Ligands: LPE.27 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.1279, A:Y.1284, A:Y.1284, A:F.1297

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 4 residues within 4Å: Chain A: G.898, G.901, L.905, F.908 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.905, A:F.908

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

LPE.7: 5 residues within 4Å: Chain A: L.793, M.797, F.806 Ligands: Y01.5, LPE.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.793, A:L.793 Salt bridges: A:H.799 LPE.8: 7 residues within 4Å: Chain A: N.1766, P.1767, S.1768, F.1772, V.1775, I.1779 Ligands: PCW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.1772, A:V.1775, A:I.1779 Hydrogen bonds: A:N.1766, A:P.1767, A:S.1768 LPE.10: 3 residues within 4Å: Ligands: Y01.5, LPE.7, PCW.11 No protein-ligand interaction detected (PLIP) LPE.12: 10 residues within 4Å: Chain A: S.1322, T.1325, L.1326, V.1688, Y.1692, F.1695, N.1699, V.1769, F.1772 Ligands: LPE.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.1688, A:Y.1692 Hydrogen bonds: A:N.1699, A:N.1699 LPE.13: 7 residues within 4Å: Chain A: A.1291, W.1292, L.1326, V.1345, N.1346, F.1695 Ligands: LPE.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1326, A:F.1695 LPE.17: 6 residues within 4Å: Chain A: L.422, T.1509, Q.1512, Y.1515, L.1678 Ligands: LPE.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.422 Hydrogen bonds: A:Q.1512 LPE.18: 7 residues within 4Å: Chain A: E.1511, Y.1515, A.1518, M.1519 Ligands: PCW.15, LPE.17, PCW.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.1511 LPE.19: 10 residues within 4Å: Chain A: D.354, K.410, T.411, M.413, G.1682, F.1686, G.1719, M.1722, I.1723 Ligands: LPE.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1686 Hydrogen bonds: A:K.410 LPE.20: 7 residues within 4Å: Chain A: Y.1249, T.1717, F.1718, G.1719, N.1720 Ligands: LPE.19, LPE.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.1717, A:G.1719, A:N.1720 Salt bridges: A:K.1253 pi-Cation interactions: A:Y.1249 LPE.21: 10 residues within 4Å: Chain A: S.1240, A.1244, F.1245, D.1247, K.1253, F.1338, F.1686, L.1687, F.1690 Ligands: LPE.20 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1338, A:F.1686, A:L.1687, A:F.1690 Salt bridges: A:D.1247 LPE.22: 5 residues within 4Å: Chain A: I.284, V.287, S.291, M.1563, I.1664 No protein-ligand interaction detected (PLIP) LPE.27: 8 residues within 4Å: Chain A: W.1212, W.1213, R.1216, Y.1284 Ligands: Y01.26, LPE.28, LPE.29, LPE.30 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1284 Salt bridges: A:R.1216 pi-Cation interactions: A:W.1213 LPE.28: 3 residues within 4Å: Chain A: K.1285 Ligands: LPE.27, LPE.29 No protein-ligand interaction detected (PLIP) LPE.29: 12 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 Ligands: LPE.27, LPE.28 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1212, A:W.1279, A:I.1280, A:Y.1284, A:Y.1284 Salt bridges: A:R.1216 pi-Cation interactions: A:Y.1220 LPE.30: 3 residues within 4Å: Chain A: G.1209, W.1212 Ligands: LPE.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.1209 LPE.34: 8 residues within 4Å: Chain A: I.1222, H.1225, W.1227, F.1228, F.1231 Chain B: W.173, E.177, C.181 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:E.177 Hydrogen bonds: A:F.1228 LPE.39: 6 residues within 4Å: Chain A: I.1211 Chain B: V.175, M.178, I.179, Y.182, K.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.178 Salt bridges: B:K.183

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

1PW.9: 13 residues within 4Å: Chain A: I.1352, I.1355, M.1356, L.1359, T.1438, L.1483, F.1486, S.1731, I.1778, I.1779, F.1782, L.1783 Ligands: PCW.11 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.1352, A:L.1359, A:T.1438, A:L.1483, A:F.1486, A:F.1486, A:F.1782, A:L.1783, A:L.1783 Hydrogen bonds: A:S.1731, A:S.1731

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

PCW.11: 14 residues within 4Å: Chain A: C.1362, L.1363, W.1366, N.1425, G.1427, L.1428, L.1431, F.1486, I.1771, I.1779 Ligands: Y01.5, LPE.8, 1PW.9, LPE.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1363, A:W.1366, A:W.1366, A:L.1428, A:L.1431, A:F.1486, A:I.1771, A:I.1779 PCW.14: 8 residues within 4Å: Chain A: Y.373, Y.375, S.382, W.383, F.389, Q.975, L.979, M.983 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.383, A:F.389, A:L.979, A:M.983 Hydrogen bonds: A:S.382, A:Q.975 PCW.15: 15 residues within 4Å: Chain A: F.288, C.289, G.1523, G.1611, W.1612, F.1615, V.1658, R.1665, T.1666, L.1668, F.1669, L.1675, A.1800 Ligands: PCW.16, LPE.18 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.288, A:W.1612, A:W.1612, A:W.1612, A:F.1615, A:F.1615, A:V.1658, A:L.1668, A:L.1675 Salt bridges: A:R.1665 PCW.16: 10 residues within 4Å: Chain A: L.1522, T.1609, V.1610, G.1611, I.1614, F.1615, V.1618, L.1648 Ligands: PCW.15, PCW.31 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1615, A:F.1615, A:V.1618 Hydrogen bonds: A:G.1611 PCW.31: 4 residues within 4Å: Chain A: I.1622 Ligands: PCW.16, LPE.18, PCW.32 No protein-ligand interaction detected (PLIP) PCW.32: 3 residues within 4Å: Chain A: F.1608 Ligands: PCW.31, P5S.33 No protein-ligand interaction detected (PLIP)

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

P5S.33: 5 residues within 4Å: Chain A: V.1597, L.1600, I.1601, H.1605 Ligands: PCW.32 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.1597, A:L.1600 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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