SMTL ID : 8vyk.1

Structure of full-length human cardiac sodium channel - Class-II.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.90 Å

Oligo State

monomer

Ligands

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

NAG-NAG-NAG-NAG-NAG.1: 5 residues within 4Å: Chain A: H.278, L.304, D.305, N.328, C.341 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: S.873, T.1376 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1379, N.1380, Q.1383 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1365, T.1367, E.1368, T.1390, E.1392 No protein-ligand interaction detected (PLIP)

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

6OU.5: 1 residues within 4Å: Chain A: H.738 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.738 6OU.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

7 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 4 residues within 4Å: Chain A: W.193, W.195, L.196, L.224 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.193, A:W.195, A:L.196, A:L.196, A:L.224 Y01.7: 5 residues within 4Å: Chain A: A.217, T.220, V.856, L.860, L.914 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.220, A:V.856, A:L.860, A:L.860, A:L.914 Y01.8: 2 residues within 4Å: Chain A: I.783, L.813 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.783, A:I.783, A:L.813 Y01.9: 6 residues within 4Å: Chain A: F.810, Y.1442, N.1443, Y.1445, M.1446, Y.1449 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.810, A:Y.1445 Hydrogen bonds: A:N.1443 Y01.10: 3 residues within 4Å: Chain A: F.885, F.888 Ligands: Y01.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.888, A:F.888, A:F.888 Y01.11: 5 residues within 4Å: Chain A: C.145, V.146, Q.150, F.884 Ligands: Y01.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.884, A:F.884 Y01.12: 7 residues within 4Å: Chain A: L.409, A.413, F.934, L.935, L.1462, I.1768, I.1771 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:A.413, A:F.934, A:L.935, A:L.1462, A:I.1768, A:I.1771

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

NAG.13: 1 residues within 4Å: Chain A: N.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.318 NAG.14: 2 residues within 4Å: Chain A: N.283, E.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.283, A:E.337 NAG.15: 1 residues within 4Å: Chain A: N.291 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, R. et al., Structure of full-length human cardiac sodium channel - Model III. To Be Published

Release Date

2025-02-12

Peptides

Sodium channel protein type 5 subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein type 5 subunit alpha

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