SMTL ID : 5xaw.1

Parallel homodimer structures of voltage-gated sodium channel beta4 for cell-cell adhesion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.1: 9 residues within 4Å: Chain A: H.36, F.37, R.38, F.47, E.52, G.53, T.54, T.65, H.103 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.38, A:R.38, A:T.65, A:T.65 P33.5: 9 residues within 4Å: Chain B: H.36, F.37, R.38, F.47, E.52, G.53, T.54, T.65, H.103 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.38, B:R.38, B:T.65

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 9 residues within 4Å: Chain A: Y.41, K.48, L.50, D.68, D.69, R.71, S.95, D.96, Y.100 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.48, A:D.68, A:D.69 PG4.3: 7 residues within 4Å: Chain A: T.10, D.11, I.12 Chain B: A.9, T.10, D.11, I.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.10, A:D.11, B:D.11 Water bridges: A:D.11 PG4.6: 11 residues within 4Å: Chain B: Y.41, K.48, L.50, D.68, D.69, R.71, I.72, L.89, S.95, D.96, Y.100 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.48, B:D.69, B:R.71, B:D.96, B:Y.100

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.17, T.18, E.19, R.90, D.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.91 GOL.7: 5 residues within 4Å: Chain B: G.17, T.18, E.19, R.90, D.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.18, B:D.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, H. et al., Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel beta 4 subunit explain its role in cell-cell adhesion. J. Biol. Chem. (2017)

Release Date

2017-07-05

Peptides

Sodium channel subunit beta-4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sodium channel subunit beta-4