SMTL ID : 8i5g.1

Structure of human Nav1.7 in complex with PF-05089771

Coordinates

PDB Format

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: 6 residues within 4Å: Chain A: F.54, E.56, R.72, Y.124, L.126, N.135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.124 Hydrogen bonds: A:R.72, A:R.72 NAG-NAG.2: 5 residues within 4Å: Chain C: N.1352, T.1354, D.1355, F.1359, S.1377 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: P.1365, N.1366, E.1369, K.1423 No protein-ligand interaction detected (PLIP)

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

NAG.4: 4 residues within 4Å: Chain A: V.91, N.93, R.96, F.107 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 NAG.5: 2 residues within 4Å: Chain A: G.33, N.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.33, A:N.110 NAG.6: 3 residues within 4Å: Chain A: R.89, T.112, N.114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.112 Hydrogen bonds: A:N.114 NAG.7: 1 residues within 4Å: Chain C: N.283 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain C: N.1375 No protein-ligand interaction detected (PLIP)

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.8: 11 residues within 4Å: Chain C: V.755, T.758, L.759, V.842, L.845, S.848, W.849, P.850, E.981, I.1330, L.1333 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.755, C:T.758, C:L.759, C:V.842, C:L.845, C:W.849, C:W.849, C:W.849, C:P.850, C:I.1330, C:I.1330, C:L.1333 Hydrogen bonds: C:E.981 Y01.25: 11 residues within 4Å: Chain C: L.759, A.762, H.765, P.767, L.1329, I.1330, N.1391, V.1392, G.1393, Y.1396 Ligands: PCW.14 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.759, C:L.1329, C:I.1330, C:V.1392, C:V.1392 Hydrogen bonds: C:N.1391 Salt bridges: C:H.765

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 C: L.398, A.402, E.406, Q.410, L.960, F.963, L.964, L.967, L.968, I.1453, I.1457, Y.1755, I.1759, F.1763 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.398, C:A.402, C:F.963, C:L.964, C:L.967, C:L.968, C:I.1453, C:I.1457, C:I.1457, C:Y.1755, C:I.1759, C:F.1763 Hydrogen bonds: C:Q.410

1 x T70: PF-05089771(Non-covalent)

T70.11: 16 residues within 4Å: Chain C: E.1545, Y.1548, W.1549, N.1551, V.1552, S.1589, G.1592, M.1593, D.1597, E.1600, F.1609, I.1612, R.1613, A.1615, R.1616, R.1619 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:D.1597 Hydrogen bonds: C:D.1597, C:R.1613, C:R.1619, C:R.1619 pi-Stacking: C:Y.1548

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

NA.12: 5 residues within 4Å: Chain C: D.361, E.927, W.928, I.929, E.930 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:W.928, C:I.929, C:E.930 Water bridges: C:R.922, C:E.927

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

LPE.13: 8 residues within 4Å: Chain C: P.1733, S.1734, I.1737, F.1738, V.1741, S.1742, I.1746 Ligands: PCW.14 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.1737, C:F.1738, C:F.1738, C:V.1741, C:I.1746 LPE.15: 8 residues within 4Å: Chain C: L.1295, I.1657, Y.1658, F.1661, V.1735, F.1738, Y.1739 Ligands: LPE.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.1658 pi-Cation interactions: C:F.1661 LPE.16: 10 residues within 4Å: Chain C: N.1256, A.1257, W.1258, L.1295, L.1298, L.1301, V.1311, N.1312, I.1315 Ligands: LPE.15 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.1295, C:L.1298 LPE.19: 9 residues within 4Å: Chain C: F.387, E.1477, Q.1478, Y.1481, L.1641, P.1642, F.1645, M.1754 Ligands: LPE.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.387, C:F.387 Hydrogen bonds: C:Q.1478 Salt bridges: C:E.1477 LPE.20: 7 residues within 4Å: Chain C: Y.1481, A.1484, M.1485, L.1488 Ligands: PCW.18, LPE.19, PCW.23 No protein-ligand interaction detected (PLIP) LPE.21: 7 residues within 4Å: Chain C: T.319, D.320, K.376, T.377, M.379, M.1655, F.1692 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.1692 Hydrogen bonds: C:T.377 LPE.22: 10 residues within 4Å: Chain C: L.1203, S.1206, G.1207, A.1210, F.1211, K.1219, M.1307, L.1649, F.1656, F.1684 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.1203, C:L.1649, C:F.1656 Hydrogen bonds: C:A.1210 LPE.26: 9 residues within 4Å: Chain A: W.173, E.177, C.181 Chain C: K.1187, I.1188, H.1191, W.1193, F.1194, F.1197 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:F.1194, A:E.177 pi-Cation interactions: C:H.1191 Salt bridges: A:E.177

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

PCW.14: 13 residues within 4Å: Chain C: C.1328, L.1329, W.1332, N.1391, G.1393, L.1394, Y.1396, L.1400, I.1737, V.1741, I.1745 Ligands: LPE.13, Y01.25 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.1329, C:L.1329, C:W.1332, C:W.1332, C:L.1394, C:Y.1396, C:L.1400, C:I.1737, C:V.1741 PCW.17: 13 residues within 4Å: Chain C: Y.339, G.340, Y.341, S.348, W.349, F.355, Q.941, A.942, L.945, M.949, M.950, V.953, I.954 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.349, C:F.355, C:F.355, C:A.942, C:L.945, C:V.953, C:I.954 Hydrogen bonds: C:S.348, C:Q.941 PCW.18: 14 residues within 4Å: Chain C: L.1488, K.1491, Q.1494, T.1575, V.1576, G.1577, I.1580, F.1581, V.1584, L.1614, I.1617, G.1618 Ligands: LPE.20, PCW.23 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.1580, C:F.1581, C:I.1617 Hydrogen bonds: C:G.1577 Salt bridges: C:K.1491 PCW.23: 4 residues within 4Å: Chain C: K.1491 Ligands: PCW.18, LPE.20, PCW.24 No protein-ligand interaction detected (PLIP) PCW.24: 8 residues within 4Å: Chain C: H.1571, F.1574, F.1583, V.1584, I.1587, I.1588, V.1591 Ligands: PCW.23 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.1574, C:F.1583, C:V.1584, C:I.1587, C:I.1587, C:I.1588, C:V.1591

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 subunit beta-1: A
Sodium channel subunit beta-2: B
Sodium channel protein type 9 subunit alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel subunit beta-1

Sodium channel subunit beta-2

Sodium channel protein type 9 subunit alpha

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