SMTL ID : 8vyj.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 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: 6 residues within 4Å: Chain A: L.304, D.305, N.328, R.340, C.341, L.342 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.305

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: 3 residues within 4Å: Chain A: D.872, N.1374, T.1376 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: N.1380, S.1382 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.1365, T.1367, E.1368, E.1392, L.1393 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: 2 residues within 4Å: Chain A: H.738, N.1404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.1404 Salt bridges: A:H.738, 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: P.192, W.193, W.195, F.221 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.192, A:W.193, A:F.221 Y01.7: 1 residues within 4Å: Chain A: L.860 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.860 Y01.8: 5 residues within 4Å: Chain A: Q.779, G.780, I.783, I.787, F.810 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.783, A:I.787, A:F.810 Y01.9: 7 residues within 4Å: Chain A: F.810, N.1443, Y.1445, I.1448, Y.1449, I.1452 Ligands: Y01.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.1448, A:I.1452 Hydrogen bonds: A:N.1443 Y01.10: 5 residues within 4Å: Chain A: F.884, F.888, Y.1445, I.1448 Ligands: Y01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.884, A:F.888 Y01.11: 4 residues within 4Å: Chain A: V.146, Q.150, F.851, F.884 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.146, A:F.851, A:F.884 Hydrogen bonds: A:Q.150 Y01.12: 8 residues within 4Å: Chain A: L.409, F.934, L.935, L.938, L.1462, I.1466, I.1768, I.1771 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.934, A:F.934, A:L.935, A:L.938, A:I.1466, 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 No protein-ligand interaction detected (PLIP) 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Biswas, R. et al., Structure of full-length human cardiac sodium channel - Model II. 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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