- Coordinates
- PDB Format
- 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)
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 4 x CLR: CHOLESTEROL(Non-covalent)
CLR.6: 8 residues within 4Å:- Chain A: I.262, P.263, G.898, G.901, N.902, M.904, L.905, F.908
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.262, A:L.905, A:F.908
CLR.23: 11 residues within 4Å:- Chain A: F.1369, M.1372, L.1376, Y.1463, S.1464, L.1465, Y.1466, M.1467, I.1469, Y.1470, F.1473
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:L.1376, A:L.1376, A:Y.1466, A:Y.1470, A:F.1473
CLR.24: 4 residues within 4Å:- Chain A: F.1288, T.1289, A.1291, W.1294
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:A.1291, A:W.1294, A:W.1294, A:W.1294
CLR.25: 6 residues within 4Å:- Chain A: Y.1284, K.1285, F.1288, F.1297
- Ligands: LPE.26, LPE.27
6 PLIP interactions:6 interactions with chain A- Hydrophobic interactions: A:Y.1284, A:Y.1284, A:K.1285, A:K.1285, A:F.1288, A:F.1288
- 18 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)
LPE.7: 5 residues within 4Å:- Chain A: M.797, H.799, F.806
- Ligands: Y01.5, LPE.10
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:H.799
LPE.8: 9 residues within 4Å:- Chain A: N.1766, P.1767, S.1768, I.1771, F.1772, V.1775, I.1779
- Ligands: 1PW.9, PCW.11
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:F.1772, A:V.1775, A:I.1779
- Hydrogen bonds: A:S.1768, A:S.1768
LPE.10: 3 residues within 4Å:- Ligands: Y01.5, LPE.7, PCW.11
No protein-ligand interaction detected (PLIP)LPE.12: 13 residues within 4Å:- Chain A: S.1322, T.1325, L.1335, L.1684, V.1688, I.1691, Y.1692, F.1695, N.1699, V.1769, F.1772, Y.1773
- Ligands: LPE.13
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:L.1335, A:L.1684, A:V.1688, A:I.1691, A:Y.1692, A:Y.1773
- Hydrogen bonds: A:N.1699, A:N.1699
LPE.13: 9 residues within 4Å:- Chain A: A.1291, W.1292, L.1295, L.1329, V.1345, N.1346, I.1349, F.1695
- Ligands: LPE.12
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.1329, A:L.1329, A:F.1695
LPE.17: 9 residues within 4Å:- Chain A: E.1339, T.1509, E.1511, Q.1512, Y.1515, L.1675, P.1676, L.1678, F.1679
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.1675, A:F.1679
- Hydrogen bonds: A:Q.1512
- Salt bridges: A:E.1339
LPE.18: 3 residues within 4Å:- Chain A: Y.1515, A.1518
- Ligands: PCW.30
No protein-ligand interaction detected (PLIP)LPE.19: 9 residues within 4Å:- Chain A: D.354, K.410, M.413, F.421, G.1682, G.1719, M.1722, I.1723
- Ligands: LPE.20
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.421
- Salt bridges: A:D.354
LPE.20: 9 residues within 4Å:- Chain A: D.1247, Y.1249, R.1252, K.1253, T.1717, F.1718, G.1719
- Ligands: LPE.19, LPE.21
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.1718
- Hydrogen bonds: A:K.1253
LPE.21: 10 residues within 4Å:- Chain A: L.1237, S.1240, A.1244, F.1245, F.1338, L.1683, F.1686, L.1687, F.1690
- Ligands: LPE.20
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:L.1237, A:F.1338, A:L.1683, A:F.1686, A:F.1686, A:L.1687
- pi-Cation interactions: A:F.1245
LPE.22: 13 residues within 4Å:- Chain A: I.284, V.287, F.288, S.291, F.381, S.382, F.385, M.1567, L.1657, G.1660, A.1661, I.1664
- Ligands: PCW.14
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:F.385, A:F.385
LPE.26: 9 residues within 4Å:- Chain A: K.1210, W.1212, W.1213, R.1216, Y.1284
- Ligands: CLR.25, LPE.27, LPE.28, LPE.29
2 PLIP interactions:2 interactions with chain A- Salt bridges: A:R.1216
- pi-Cation interactions: A:W.1213
LPE.27: 5 residues within 4Å:- Chain A: Y.1284, K.1285
- Ligands: CLR.25, LPE.26, LPE.28
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:K.1285
LPE.28: 13 residues within 4Å:- Chain A: W.1212, W.1213, R.1216, Y.1220, W.1279, I.1280, A.1281, Y.1282, G.1283, Y.1284, K.1285
- Ligands: LPE.26, LPE.27
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.1212, A:I.1280, A:Y.1284, A:Y.1284
- Hydrogen bonds: A:R.1216
LPE.29: 2 residues within 4Å:- Chain A: W.1212
- Ligands: LPE.26
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:W.1212
LPE.32: 6 residues within 4Å:- Chain A: N.188, Y.191, T.192, G.195, I.196, F.199
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:I.196, A:F.199
- pi-Cation interactions: A:Y.191
LPE.34: 10 residues within 4Å:- Chain A: K.1221, I.1222, H.1225, W.1227, F.1228, F.1231
- Chain B: L.170, W.173, E.177, C.181
1 PLIP interactions:1 interactions with chain B- Salt bridges: B:E.177
LPE.35: 6 residues within 4Å:- Chain A: I.1211, I.1215
- Chain B: V.175, M.178, I.179, Y.182
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:M.178
- 1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)
- 6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
PCW.11: 16 residues within 4Å:- Chain A: L.1359, C.1362, L.1363, W.1366, N.1425, G.1427, L.1428, L.1431, F.1486, I.1771, V.1775, I.1779
- Ligands: Y01.5, LPE.8, 1PW.9, LPE.10
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:L.1359, A:W.1366, A:W.1366, A:L.1428, A:L.1431, A:F.1486, A:I.1771, A:V.1775, A:I.1779
PCW.14: 15 residues within 4Å:- Chain A: Y.373, G.374, Y.375, S.382, W.383, F.385, E.971, Q.975, A.976, L.979, I.980, M.983, M.984, F.987
- Ligands: LPE.22
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:W.383, A:W.383, A:F.385, A:F.385, A:A.976, A:I.980, A:M.983, A:F.987
- Hydrogen bonds: A:S.382, A:Q.975
PCW.15: 12 residues within 4Å:- Chain A: F.288, F.293, G.1523, G.1611, W.1612, F.1615, R.1665, T.1666, L.1668, F.1669, A.1800
- Ligands: PCW.16
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:F.288, A:F.293, A:F.1615, A:F.1615, A:L.1668, A:L.1668, A:L.1668
- Salt bridges: A:R.1665
PCW.16: 12 residues within 4Å:- Chain A: L.1522, T.1609, G.1611, I.1614, F.1615, V.1618, L.1648, I.1651, G.1652, M.1672
- Ligands: PCW.15, PCW.30
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:F.1615, A:V.1618, A:I.1651
- Hydrogen bonds: A:G.1611
PCW.30: 6 residues within 4Å:- Chain A: L.1522, V.1618, I.1622
- Ligands: PCW.16, LPE.18, PCW.31
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:V.1618, A:I.1622
PCW.31: 6 residues within 4Å:- Chain A: F.1608, V.1618, I.1621, I.1622
- Ligands: PCW.30, P5S.33
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.1608, A:V.1618, A:I.1621
- 1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, G. et al., Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7. Proc.Natl.Acad.Sci.USA (2022)
- Release Date
- 2022-08-10
- 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
AB
BC
C - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- 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)
- 7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 4 x CLR: CHOLESTEROL(Non-covalent)
- 18 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)
- 1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)
- 6 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Huang, G. et al., Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7. Proc.Natl.Acad.Sci.USA (2022)
- Release Date
- 2022-08-10
- 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
AB
BC
C - Membrane
-
We predict this structure to be a membrane protein.