SMTL ID : 5hk7.1

Bacterial sodium channel pore, 2.95 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-tetramer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: R.128 Chain B: R.128 Chain C: R.128 Chain D: R.128 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: W.110 Chain B: W.110 Chain C: W.110 Chain D: W.110 Ligand excluded by PLIP

10 x VVA: 2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate(Non-covalent)(Non-functional Binders)

VVA.2: 8 residues within 4Å: Chain A: W.79, V.83 Chain D: F.25, G.48, A.49, Y.52, F.55, M.58 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.25, D:F.55, D:F.55, A:W.79, A:V.83 VVA.3: 4 residues within 4Å: Chain A: L.21, M.58, S.90 Chain B: F.91 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.91, A:L.21 VVA.5: 11 residues within 4Å: Chain A: F.25, E.42, G.48, A.49, M.51, Y.52, F.55 Chain B: I.72, P.76, W.79, V.83 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.79, B:V.83, A:F.25, A:F.55, A:F.55 Hydrogen bonds: A:E.42 VVA.6: 10 residues within 4Å: Chain B: F.25, E.42, G.48, M.51, Y.52, F.55 Chain C: I.72, P.76, W.79 Ligands: VVA.11 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.25, B:Y.52, C:W.79 VVA.7: 3 residues within 4Å: Chain B: M.58, V.93 Chain C: L.87 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.87, B:V.93 VVA.9: 9 residues within 4Å: Chain C: F.25, E.42, G.48, M.51, Y.52 Chain D: I.72, P.76, W.79 Ligands: VVA.10 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:W.79, C:F.25, C:F.25, C:M.51 VVA.10: 2 residues within 4Å: Chain C: M.51 Ligands: VVA.9 No protein-ligand interaction detected (PLIP) VVA.11: 1 residues within 4Å: Ligands: VVA.6 No protein-ligand interaction detected (PLIP) VVA.12: 5 residues within 4Å: Chain C: M.58, T.59 Chain D: L.87, S.90, F.91 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.87, D:F.91 VVA.14: 1 residues within 4Å: Chain D: M.58 No protein-ligand interaction detected (PLIP)

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

NA.8: 2 residues within 4Å: Chain B: E.61, S.62 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.62, B:E.61, B:S.62 NA.13: 2 residues within 4Å: Chain B: T.59 Chain C: L.60 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arrigoni, C. et al., Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation. Cell (2016)

Release Date

2016-03-09

Peptides

Ion transport protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

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

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