SMTL ID : 6agf.1

Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: Q.321, W.326, W.381, N.405, E.417, C.418 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.1247, N.1248, E.1251 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.1234, T.1236, T.1237, L.1255, T.1258, Q.1260 No protein-ligand interaction detected (PLIP)

6 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.4: 10 residues within 4Å: Chain A: Y.427, S.436, W.437, F.439, L.440, F.443, Q.818, T.823, L.826 Ligands: 6OU.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.439, A:F.439, A:L.440, A:F.443, A:F.443, A:T.823, A:L.826 Hydrogen bonds: A:Y.427, A:Q.818 6OU.5: 9 residues within 4Å: Chain A: L.1207, G.1274, L.1275, P.1614, S.1615, C.1619, I.1626, I.1627 Ligands: 6OU.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.1207, A:I.1626, A:I.1626, A:I.1626, A:I.1627 Hydrogen bonds: A:S.1615 6OU.6: 19 residues within 4Å: Chain A: S.739, T.747, L.750, L.839, I.1203, L.1207, C.1210, A.1284, I.1322, I.1323, S.1326, T.1329, L.1330, F.1333, F.1629, L.1630 Ligands: 6OU.5, 6OU.7, 9Z9.10 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.750, A:L.839, A:I.1203, A:L.1207, A:I.1322, A:I.1323, A:L.1330, A:F.1333, A:F.1333, A:F.1629, A:L.1630 6OU.7: 15 residues within 4Å: Chain A: L.293, M.297, M.446, I.482, I.485, L.486, V.830, N.833, L.834, V.836, L.837 Ligands: 6OU.4, 6OU.6, 6OU.8, 9Z9.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.293, A:I.485, A:N.833, A:L.834 Hydrogen bonds: A:N.833 6OU.8: 6 residues within 4Å: Chain A: V.290, K.291, S.294, M.297, I.298 Ligands: 6OU.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.290, A:I.298 Hydrogen bonds: A:S.294 Salt bridges: A:K.291 6OU.9: 7 residues within 4Å: Chain A: L.185, C.188, T.192, M.193, F.755, F.794, L.1316 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.185, A:T.192, A:F.755, A:F.794, A:L.1316

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.10: 16 residues within 4Å: Chain A: L.486, A.490, F.840, L.841, F.848, L.1330, I.1338, N.1342, F.1629, Y.1636, I.1637, I.1640, L.1641, F.1644 Ligands: 6OU.6, 6OU.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.486, A:A.490, A:F.840, A:L.841, A:I.1338, A:F.1629, A:Y.1636, A:Y.1636, A:I.1637, A:I.1640, A:I.1640 Hydrogen bonds: A:N.1342

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

NAG.11: 2 residues within 4Å: Chain B: G.33, N.110 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain B: N.114 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, X. et al., Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta 1. Science (2018)

Release Date

2018-10-10

Peptides

Sodium channel protein type 4 subunit alpha: A
Sodium channel subunit beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 4 subunit alpha

Sodium channel subunit beta-1

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