SMTL ID : 4x89.1 (1 other biounit)

NavMs voltage-gated sodium channal pore and C-terminal domain soaked with Silver nitrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-tetramer

Ligands

4 x 2CV: HEGA-10(Non-covalent)

2CV.1: 10 residues within 4Å: Chain A: M.64, P.68, N.69, W.71, I.75 Chain B: F.17, S.40, K.41, Y.44, F.47 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:W.71, A:I.75, B:F.17, B:Y.44, B:F.47 Hydrogen bonds: A:P.68, B:S.40, B:S.40 Water bridges: A:R.61 2CV.7: 9 residues within 4Å: Chain B: M.64, P.68, N.69, W.71 Chain C: F.17, S.40, K.41, Y.44, F.47 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.17, C:F.47, B:W.71, B:W.71 Hydrogen bonds: C:S.40, C:S.40, B:P.68 Water bridges: B:R.61 2CV.9: 10 residues within 4Å: Chain C: M.64, P.68, N.69, W.71, I.75 Chain D: F.17, S.40, K.41, Y.44, F.47 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.17, D:Y.44, D:F.47, C:W.71, C:I.75 Hydrogen bonds: D:S.40, D:S.40, C:P.68 Water bridges: C:R.61 2CV.15: 9 residues within 4Å: Chain A: F.17, S.40, K.41, Y.44, F.47 Chain D: M.64, P.68, N.69, W.71 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:W.71, D:W.71, A:F.17, A:F.47 Hydrogen bonds: D:P.68, A:S.40, A:S.40 Water bridges: D:R.61

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 7 residues within 4Å: Chain A: M.23, L.27, Y.28, N.69, A.70, V.72, F.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 1PE.8: 6 residues within 4Å: Chain B: M.23, Y.28, N.69, A.70, V.72, F.73 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.69 1PE.10: 7 residues within 4Å: Chain C: M.23, L.27, Y.28, N.69, A.70, V.72, F.73 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.28, C:Y.28 1PE.16: 6 residues within 4Å: Chain D: M.23, Y.28, N.69, A.70, V.72, F.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.28, D:N.69

8 x NA: SODIUM ION(Non-functional Binders)

NA.3: 7 residues within 4Å: Chain A: S.54 Chain B: S.54 Chain C: S.54 Chain D: S.54 Ligands: NA.4, NA.11, NA.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.54 NA.4: 5 residues within 4Å: Ligands: NA.3, NA.5, NA.11, NA.12, NA.13 No protein-ligand interaction detected (PLIP) NA.5: 3 residues within 4Å: Ligands: NA.4, NA.12, NA.13 No protein-ligand interaction detected (PLIP) NA.6: 1 residues within 4Å: Ligands: NA.14 No protein-ligand interaction detected (PLIP) NA.11: 7 residues within 4Å: Chain A: S.54 Chain B: S.54 Chain C: S.54 Chain D: S.54 Ligands: NA.3, NA.4, NA.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.54 NA.12: 5 residues within 4Å: Ligands: NA.3, NA.4, NA.5, NA.11, NA.13 No protein-ligand interaction detected (PLIP) NA.13: 3 residues within 4Å: Ligands: NA.4, NA.5, NA.12 No protein-ligand interaction detected (PLIP) NA.14: 1 residues within 4Å: Ligands: NA.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Naylor, C.E. et al., Molecular basis of ion permeability in a voltage-gated sodium channel. Embo J. (2016)

Release Date

2016-03-09

Peptides

Ion transport protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Membrane

We predict this structure to be a membrane protein.
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Ion transport protein

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