SMTL ID : 8i5x.1

Structure of human Nav1.7 in complex with Vinpocetine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-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: 5 residues within 4Å: Chain A: N.1392, T.1394, D.1395, F.1399, S.1417 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.1405, N.1406, E.1409, K.1463 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, L.126, 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.10: 1 residues within 4Å: Chain A: N.1415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1415 NAG.29: 4 residues within 4Å: Chain B: V.91, N.93, R.96, F.107 No protein-ligand interaction detected (PLIP) NAG.30: 2 residues within 4Å: Chain B: G.33, N.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33, B:N.110 NAG.31: 2 residues within 4Å: Chain B: T.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.112 Hydrogen bonds: B:N.114

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

P5S.5: 10 residues within 4Å: Chain A: W.1218, W.1219, R.1222, Y.1226, W.1285, I.1286, A.1287, G.1289, Y.1290 Ligands: LPE.25 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1218, A:W.1218, A:W.1285, A:I.1286, A:Y.1290 Salt bridges: A:R.1222, A:R.1222

5 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 4 residues within 4Å: Chain A: T.1295, A.1297, L.1304 Ligands: Y01.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.1295, A:A.1297, A:L.1304 Y01.7: 5 residues within 4Å: Chain A: Y.1290, K.1291, F.1294, T.1295 Ligands: Y01.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.1290, A:Y.1290, A:K.1291, A:F.1294, A:F.1294 Y01.8: 10 residues within 4Å: Chain A: V.795, T.798, L.799, S.888, W.889, P.890, E.1021, L.1028, I.1370, L.1373 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.795, A:T.798, A:L.799, A:W.889, A:W.889, A:W.889, A:L.1028, A:I.1370, A:L.1373 Hydrogen bonds: A:E.1021 Y01.11: 2 residues within 4Å: Chain A: Y.1469, Y.1472 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1472 Hydrogen bonds: A:Y.1469, A:Y.1469 Y01.28: 8 residues within 4Å: Chain A: L.799, A.802, H.805, P.807, N.1431, G.1433, Y.1436 Ligands: PCW.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.799, A:P.807, A:N.1431, A:Y.1436 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: 14 residues within 4Å: Chain A: L.438, A.442, E.446, Q.450, L.1000, F.1003, L.1004, L.1007, L.1008, S.1012, I.1493, I.1497, I.1799, F.1803 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.438, A:A.442, A:L.1000, A:F.1003, A:F.1003, A:L.1007, A:L.1008, A:I.1493, A:I.1493, A:I.1497, A:I.1799, A:I.1799

1 x T7F: Vinpocetine(Non-covalent)

T7F.12: 9 residues within 4Å: Chain A: W.1372, A.1443, T.1444, T.1488, L.1489, S.1737, I.1784, F.1788 Ligands: PCW.14 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.1372, A:T.1488, A:L.1489, A:F.1788, A:F.1788 pi-Stacking: A:F.1788, A:F.1788

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

LPE.13: 8 residues within 4Å: Chain A: S.1750, P.1773, S.1774, I.1777, F.1778, V.1781, S.1782 Ligands: PCW.14 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1777, A:F.1778, A:F.1778, A:V.1781 Hydrogen bonds: A:S.1750, A:S.1750 LPE.15: 7 residues within 4Å: Chain A: L.1335, Y.1698, F.1701, V.1775, F.1778, Y.1779 Ligands: LPE.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1698 pi-Cation interactions: A:F.1701 LPE.16: 9 residues within 4Å: Chain A: A.1297, W.1298, L.1332, L.1335, L.1338, V.1351, N.1352, I.1355 Ligands: LPE.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1332, A:L.1335, A:L.1338 LPE.19: 11 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 Ligands: LPE.20 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.427, A:L.1681 Hydrogen bonds: A:Q.1518 pi-Cation interactions: A:Y.1521 LPE.20: 8 residues within 4Å: Chain A: K.1520, Y.1521, A.1524, M.1525, K.1527, L.1528, L.1681 Ligands: LPE.19 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1681 LPE.21: 10 residues within 4Å: Chain A: T.359, D.360, K.416, T.417, M.419, F.1692, M.1695, G.1725, M.1728 Ligands: LPE.22 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.1692 Hydrogen bonds: A:D.360 LPE.22: 7 residues within 4Å: Chain A: D.1253, Y.1255, R.1258, T.1723, G.1725 Ligands: LPE.21, LPE.23 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.1253, A:Y.1255 Salt bridges: A:K.416 LPE.23: 11 residues within 4Å: Chain A: L.1243, S.1246, G.1247, A.1250, F.1251, F.1344, M.1347, L.1689, F.1696, F.1724 Ligands: LPE.22 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.1243, A:F.1344, A:L.1689, A:F.1696 Hydrogen bonds: A:A.1250 LPE.24: 8 residues within 4Å: Chain A: V.293, S.297, M.1569, M.1573, L.1663, G.1666, A.1667, I.1670 No protein-ligand interaction detected (PLIP) LPE.25: 5 residues within 4Å: Chain A: W.1218, W.1219, R.1222, Y.1290 Ligands: P5S.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.1222 LPE.32: 10 residues within 4Å: Chain A: K.1227, I.1228, H.1231, W.1233, F.1234, F.1237 Chain B: W.173, L.174, E.177, C.181 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:F.1234 Salt bridges: A:H.1231, B:E.177 pi-Cation interactions: A:H.1231

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

PCW.14: 12 residues within 4Å: Chain A: C.1368, L.1369, W.1372, N.1431, G.1433, L.1434, Y.1436, L.1440, I.1777 Ligands: T7F.12, LPE.13, Y01.28 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.1369, A:W.1372, A:Y.1436, A:Y.1436, A:L.1440, A:L.1440, A:I.1777 Hydrogen bonds: A:N.1431 PCW.17: 14 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.389, A:F.391, A:L.392, A:F.395, A:F.395, A:L.985, A:I.986, A:M.989, A:V.993 Hydrogen bonds: A:S.388, A:Q.981 PCW.18: 13 residues within 4Å: Chain A: L.1528, K.1531, F.1614, T.1615, G.1617, I.1620, F.1621, V.1624, I.1628, L.1654, G.1658, M.1678 Ligands: PCW.26 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.1620, A:F.1621, A:F.1621, A:V.1624, A:I.1628 Hydrogen bonds: A:G.1617 Salt bridges: A:K.1531 PCW.26: 15 residues within 4Å: Chain A: V.298, L.1528, G.1529, K.1531, G.1617, W.1618, F.1621, L.1661, V.1664, R.1671, L.1674, F.1675, L.1677, M.1678 Ligands: PCW.18 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.298, A:F.1621, A:F.1621, A:L.1661, A:V.1664, A:L.1674, A:L.1674, A:L.1677 Salt bridges: A:R.1671 PCW.27: 7 residues within 4Å: Chain A: H.1611, F.1614, F.1623, V.1624, I.1627, I.1628, V.1631 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.1614, A:F.1623, A:V.1624, A:V.1624, A:I.1627, A:I.1627, A:I.1628, A:V.1631

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
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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