SMTL ID : 8j4f.1

Structure of human Nav1.7 in complex with Hardwickii acid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

3 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: P.1405, N.1406, E.1409, K.1463 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.1392, T.1394, D.1395 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

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

NAG.4: 1 residues within 4Å: Chain A: N.323 No protein-ligand interaction detected (PLIP) NAG.5: 1 residues within 4Å: Chain A: N.1415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1415 NAG.24: 4 residues within 4Å: Chain B: G.33, M.34, T.109, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.25: 3 residues within 4Å: Chain B: R.89, T.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.89, B:N.114 NAG.26: 3 residues within 4Å: Chain B: V.91, N.93, R.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96

1 x UK0: (4~{a}~{R},5~{S},6~{R},8~{a}~{R})-5-[2-(furan-3-yl)ethyl]-5,6,8~{a}-trimethyl-3,4,4~{a},6,7,8-hexahydronaphthalene-1-carboxylic acid(Non-covalent)

UK0.6: 11 residues within 4Å: Chain A: L.1365, W.1372, A.1443, T.1444, G.1484, S.1485, T.1488, L.1489, F.1492, F.1788 Ligands: PCW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1372, A:A.1443, A:T.1444, A:L.1489, A:F.1492, A:F.1788

3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 4 residues within 4Å: Chain A: T.1295, A.1297, W.1300, L.1304 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.1295, A:A.1297, A:W.1300, A:L.1304 Y01.8: 9 residues within 4Å: Chain A: V.795, T.798, S.888, W.889, P.890, E.1021, L.1028, I.1370, L.1373 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.795, A:T.798, A:W.889, A:W.889, A:W.889, A:L.1028, A:I.1370, A:I.1370, A:L.1373 Y01.23: 8 residues within 4Å: Chain A: L.799, H.805, P.807, L.1373, N.1431, V.1432, G.1433 Ligands: PCW.11 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1373, A:N.1431, A:V.1432, A:V.1432 Hydrogen bonds: A:N.1431 Salt bridges: A:H.805

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

9Z9.9: 13 residues within 4Å: Chain A: L.438, E.446, Q.450, L.1000, F.1003, L.1004, L.1007, L.1008, S.1012, I.1493, I.1497, I.1799, F.1803 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.1000, A:F.1003, A:F.1003, A:L.1004, A:L.1007, A:L.1008, A:I.1493, A:I.1493, A:I.1497, A:I.1497, A:I.1799

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

LPE.10: 8 residues within 4Å: Chain A: P.1773, S.1774, I.1777, F.1778, V.1781, S.1782, I.1785 Ligands: PCW.11 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.1777, A:F.1778, A:F.1778, A:F.1778, A:V.1781, A:I.1785, A:I.1785 LPE.12: 9 residues within 4Å: Chain A: L.1335, L.1338, V.1694, I.1697, Y.1698, F.1701, F.1778, S.1782 Ligands: LPE.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1698 pi-Cation interactions: A:F.1701 LPE.13: 7 residues within 4Å: Chain A: A.1297, W.1298, L.1338, V.1351, N.1352, I.1355 Ligands: LPE.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1338 LPE.16: 10 residues within 4Å: Chain A: F.427, E.1517, Q.1518, Y.1521, L.1681, P.1682, L.1684, F.1685, G.1688, M.1794 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.427, A:F.427, A:L.1681 Hydrogen bonds: A:Q.1518 pi-Cation interactions: A:Y.1521 LPE.17: 9 residues within 4Å: Chain A: T.359, D.360, K.416, T.417, M.419, V.423, M.1695, M.1728 Ligands: LPE.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.423 Hydrogen bonds: A:K.416 LPE.18: 6 residues within 4Å: Chain A: D.1253, Y.1255, R.1258, T.1723 Ligands: LPE.17, LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.1253 Salt bridges: A:K.416 LPE.19: 10 residues within 4Å: Chain A: L.1243, S.1246, G.1247, A.1250, F.1251, M.1347, L.1689, F.1696, F.1724 Ligands: LPE.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1243, A:L.1689, A:F.1696 Hydrogen bonds: A:A.1250 LPE.20: 6 residues within 4Å: Chain A: V.293, S.297, M.1569, L.1663, G.1666, A.1667 No protein-ligand interaction detected (PLIP) LPE.21: 4 residues within 4Å: Chain A: W.1218, W.1219, R.1222, Y.1290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.1222 LPE.27: 9 residues within 4Å: Chain A: K.1227, I.1228, H.1231, W.1233, F.1234 Chain B: W.173, L.174, E.177, C.181 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:E.177 pi-Cation interactions: A:H.1231

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

PCW.11: 13 residues within 4Å: Chain A: C.1368, L.1369, N.1431, G.1433, L.1434, Y.1436, L.1437, L.1440, I.1777, V.1781 Ligands: UK0.6, LPE.10, Y01.23 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.1369, A:L.1434, A:Y.1436, A:L.1437, A:L.1440, A:I.1777, A:V.1781 PCW.14: 15 residues within 4Å: Chain A: Y.379, G.380, Y.381, S.388, W.389, F.391, L.392, F.395, Q.981, L.985, I.986, M.989, M.990, V.993, I.994 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.389, A:F.391, A:L.392, A:F.395, A:L.985, A:L.985, A:I.986, A:M.989, A:V.993, A:I.994 Hydrogen bonds: A:S.388, A:Q.981 PCW.15: 9 residues within 4Å: Chain A: K.1531, F.1614, T.1615, I.1620, F.1621, V.1624, I.1657, M.1678 Ligands: PCW.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1620, A:F.1621, A:I.1657 Hydrogen bonds: A:G.1617 Salt bridges: A:K.1531 PCW.22: 13 residues within 4Å: Chain A: F.294, G.1529, G.1617, W.1618, F.1621, V.1664, R.1671, T.1672, L.1674, F.1675, M.1678, V.1805 Ligands: PCW.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.294, A:W.1618, A:F.1621, A:F.1621, A:V.1664, A:L.1674, A:L.1674 Salt bridges: A:R.1671

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Q. et al., Structural mapping of Na v 1.7 antagonists. Nat Commun (2023)

Release Date

2023-06-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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