SMTL ID : 8i5b.1

Structure of human Nav1.7 in complex with bupivacaine

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.1392, T.1394, D.1395, F.1399, S.1417 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1405, N.1406, S.1408, E.1409, K.1463 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.1415 No protein-ligand interaction detected (PLIP) NAG.4: 1 residues within 4Å: Chain A: N.323 No protein-ligand interaction detected (PLIP) NAG.24: 4 residues within 4Å: Chain B: V.91, N.93, R.96, F.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 NAG.25: 3 residues within 4Å: Chain B: G.33, R.89, N.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.33, B:R.89, B:N.110 NAG.26: 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 NAG.27: 2 residues within 4Å: Chain B: Y.124, N.135 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain C: S.64, N.66, R.84, R.137 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.64, C:S.64, C:R.84, C:R.137

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

P5S.5: 9 residues within 4Å: Chain A: W.1218, W.1219, R.1222, K.1223, Y.1226, W.1285, I.1286, A.1287, Y.1290 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.1218, A:W.1285, A:I.1286, A:Y.1290, A:Y.1290 Hydrogen bonds: A:W.1219 Salt bridges: A:R.1222, A:R.1222

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 4 residues within 4Å: Chain A: T.1295, A.1297, W.1300, L.1304 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1300, A:W.1300, A:W.1300, A:W.1300, A:W.1300, A:L.1304 Y01.7: 3 residues within 4Å: Chain A: Y.1290, K.1291, T.1295 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1290, A:Y.1290, A:K.1291 Y01.8: 10 residues within 4Å: Chain A: V.795, T.798, L.799, L.885, S.888, W.889, P.890, L.1366, I.1370, L.1373 8 PLIP interactions: 8 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.1366, A:L.1373 Y01.9: 2 residues within 4Å: Chain A: Y.1472, I.1475 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1472, A:I.1475, A:I.1475 Y01.10: 11 residues within 4Å: Chain A: A.252, T.255, F.256, L.262, I.916, F.920, V.923, L.927, M.983, M.990, I.994 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.252, A:T.255, A:F.256, A:L.262, A:I.916, A:F.920, A:V.923, A:L.927, A:L.927, A:I.994, A:I.994 Y01.11: 9 residues within 4Å: Chain A: A.802, M.803, H.805, P.807, L.1369, N.1431, V.1432, G.1433 Ligands: PCW.13 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1369, A:N.1431, A:V.1432 Salt bridges: A:H.805

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

LPE.12: 8 residues within 4Å: Chain A: P.1773, S.1774, I.1777, F.1778, V.1781, S.1782, I.1785 Ligands: PCW.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1777, A:F.1778, A:F.1778, A:V.1781, A:I.1785 LPE.14: 11 residues within 4Å: Chain A: N.1296, A.1297, W.1298, L.1301, L.1332, L.1335, L.1338, L.1341, V.1351, N.1352, I.1355 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1332, A:L.1335, A:L.1335, A:L.1338 LPE.17: 7 residues within 4Å: Chain A: K.1520, Y.1521, M.1525, L.1528, M.1678, L.1681 Ligands: PCW.21 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1681 LPE.18: 9 residues within 4Å: Chain A: D.360, K.416, M.419, G.1688, L.1691, M.1695, G.1725, M.1728, I.1729 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1691 LPE.19: 10 residues within 4Å: Chain A: L.1243, G.1247, A.1250, F.1251, D.1253, K.1259, F.1692, L.1693, F.1696, F.1724 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1692, A:L.1693 Salt bridges: A:D.1253 pi-Cation interactions: A:F.1251 LPE.20: 9 residues within 4Å: Chain A: V.293, S.297, F.387, S.388, L.1663, G.1666, A.1667, I.1670 Ligands: PCW.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.387

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

PCW.13: 15 residues within 4Å: Chain A: L.1365, C.1368, L.1369, W.1372, N.1431, G.1433, L.1434, L.1437, L.1440, F.1492, I.1777, V.1781, I.1785 Ligands: Y01.11, LPE.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.1365, A:L.1369, A:L.1369, A:W.1372, A:W.1372, A:L.1434, A:L.1437, A:L.1440, A:F.1492, A:I.1777, A:V.1781, A:I.1785 PCW.15: 13 residues within 4Å: Chain A: Y.379, G.380, Y.381, S.388, W.389, F.395, Q.981, A.982, L.985, I.986, M.989, V.993 Ligands: LPE.20 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.389, A:F.395, A:A.982, A:L.985, A:I.986, A:V.993 Hydrogen bonds: A:S.388, A:Q.981 PCW.16: 10 residues within 4Å: Chain A: I.302, L.1528, T.1615, G.1617, I.1620, F.1621, V.1624, L.1654 Ligands: PCW.21, PCW.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.302, A:V.1624 Hydrogen bonds: A:G.1617 PCW.21: 2 residues within 4Å: Ligands: PCW.16, LPE.17 No protein-ligand interaction detected (PLIP) PCW.22: 13 residues within 4Å: Chain A: C.295, F.299, L.428, K.1531, Q.1534, W.1618, L.1661, R.1671, L.1674, F.1675, L.1677, M.1678 Ligands: PCW.16 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.299, A:L.428, A:W.1618, A:W.1618, A:W.1618, A:L.1661, A:L.1674, A:L.1677 Salt bridges: A:R.1671

1 x OJ0: Levobupivacaine(Non-covalent)

OJ0.23: 7 residues within 4Å: Chain A: L.1007, L.1008, G.1494, I.1497, D.1498, N.1501, L.1800 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1008, A:I.1497, A:D.1498, A:L.1800

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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