- 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)
- 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)
- 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
BB
CC
A - Membrane
-
We predict this structure to be a membrane protein.
- 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)
- 5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)
- 1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)
- 1 x T70: PF-05089771(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 8 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)
- 5 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 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
BB
CC
A - Membrane
-
We predict this structure to be a membrane protein.