- Coordinates
- PDB Format
- 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)
- 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)
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- 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)
- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 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)
- 3 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)
- 10 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 4 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 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
AB
B - Membrane
-
We predict this structure to be a membrane protein.