SMTL ID : 9iti.1

Nav1.7 with mutations that eliminate beta1 binding

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.1395, T.1397, D.1398, F.1402 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1408, N.1409, S.1411, E.1412 No protein-ligand interaction detected (PLIP)

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

NAG.3: 1 residues within 4Å: Chain A: N.326 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.1418 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.5: 6 residues within 4Å: Chain A: R.1225, Y.1229, Y.1291, Y.1293, K.1294, T.1295 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.1294 Hydrogen bonds: A:K.1294 Salt bridges: A:R.1225, A:R.1225 P5S.15: 8 residues within 4Å: Chain A: G.1532, W.1621, F.1624, L.1664, R.1674, L.1677, F.1678 Ligands: PCW.16 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1621, A:W.1621, A:F.1624, A:F.1624, A:L.1664 Hydrogen bonds: A:G.1532 Salt bridges: A:R.1674

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 3 residues within 4Å: Chain A: D.404, Y.405, E.973 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.404, A:E.973

10 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

LPE.7: 3 residues within 4Å: Chain A: F.815 Ligands: LPE.10, Y01.28 No protein-ligand interaction detected (PLIP) LPE.8: 5 residues within 4Å: Chain A: S.1776, I.1779, F.1780, S.1784 Ligands: PCW.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1780 LPE.10: 3 residues within 4Å: Chain A: L.1372 Ligands: LPE.7, Y01.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1372 LPE.12: 9 residues within 4Å: Chain A: V.1354, I.1358, I.1700, Y.1701, F.1704, V.1777, F.1780, Y.1781 Ligands: LPE.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.1354, A:I.1358 LPE.13: 5 residues within 4Å: Chain A: A.1300, W.1301, R.1351, N.1355 Ligands: LPE.12 No protein-ligand interaction detected (PLIP) LPE.17: 6 residues within 4Å: Chain A: Q.403, F.434, L.1684, F.1688, F.1735, T.1739 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.434, A:F.1735, A:T.1739 LPE.18: 4 residues within 4Å: Chain A: Y.1524, A.1527, M.1681 Ligands: PCW.22 No protein-ligand interaction detected (PLIP) LPE.19: 7 residues within 4Å: Chain A: D.363, K.419, M.422, M.1698, G.1728, M.1731, F.1735 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1735 LPE.20: 8 residues within 4Å: Chain A: S.1249, G.1250, A.1253, F.1254, D.1256, K.1262, F.1695, F.1699 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.1695 LPE.21: 4 residues within 4Å: Chain A: V.296, M.1565, L.1666, A.1670 No protein-ligand interaction detected (PLIP)

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.1364, M.1365, V.1367, L.1368, C.1371, W.1375, A.1446, T.1447, F.1448, T.1491, F.1495, I.1787, F.1790 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.1364, A:V.1367, A:L.1368, A:W.1375, A:F.1495, A:F.1495, A:F.1495, A:I.1787

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

PCW.11: 9 residues within 4Å: Chain A: N.1434, G.1436, Y.1439, L.1443, L.1751, P.1775, I.1779 Ligands: LPE.8, Y01.28 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1443, A:L.1443, A:I.1779 Hydrogen bonds: A:N.1434 PCW.14: 13 residues within 4Å: Chain A: Y.382, G.383, Y.384, S.391, W.392, F.394, L.395, F.398, Q.984, L.988, I.989, M.992, M.993 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.392, A:F.394, A:F.394, A:L.395, A:F.398, A:L.988, A:I.989, A:M.992 Hydrogen bonds: A:S.391, A:Q.984 PCW.16: 8 residues within 4Å: Chain A: L.1531, K.1534, G.1620, V.1627, I.1631, M.1681 Ligands: P5S.15, PCW.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.1627, A:V.1627 Hydrogen bonds: A:G.1620 PCW.22: 6 residues within 4Å: Chain A: L.1531, I.1623, V.1627 Ligands: PCW.16, LPE.18, PCW.23 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.1623, A:V.1627 PCW.23: 5 residues within 4Å: Chain A: H.1614, F.1617, I.1623, I.1631 Ligands: PCW.22 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1617, A:I.1623, A:I.1631 Salt bridges: A:H.1614

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.24: 4 residues within 4Å: Chain A: T.1298, A.1300, W.1303, L.1307 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1300, A:W.1303, A:W.1303, A:L.1307 Y01.25: 10 residues within 4Å: Chain A: V.798, T.801, V.885, L.888, S.891, W.892, P.893, L.1369, I.1373, L.1376 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.798, A:V.798, A:V.885, A:W.892, A:W.892, A:W.892, A:W.892, A:W.892, A:P.893, A:L.1369, A:I.1373, A:I.1373, A:L.1376 Y01.27: 1 residues within 4Å: Chain A: Y.1475 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1475, A:Y.1475, A:Y.1475 Y01.28: 13 residues within 4Å: Chain A: L.802, A.805, M.806, H.808, L.1372, L.1376, N.1434, V.1435, G.1436, Y.1439 Ligands: LPE.7, LPE.10, PCW.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.802, A:A.805, A:L.1376, A:V.1435 Salt bridges: A:H.808

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.26: 11 residues within 4Å: Chain A: L.441, A.445, E.449, Q.453, F.1006, L.1007, L.1011, I.1496, I.1500, I.1801, F.1805 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.441, A:A.445, A:F.1006, A:L.1007, A:L.1011, A:I.1496, A:I.1496, A:I.1801, A:I.1801, A:F.1805, A:F.1805, A:F.1805, A:F.1805 Hydrogen bonds: A:Q.453

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, T. et al., Critical role of extracellular loops in differential modulations of TTX-sensitive and TTX-resistant Na v channels. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-08-20

Peptides

Sodium channel protein type 9 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 9 subunit alpha