SMTL ID : 6zfm.1

Structure of alpha-Cobratoxin with a peptide inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

2 x TYR- MET- TRP- ASP- GLY- TRP- TYR- MET: peptide 12(Non-covalent)

TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.1: 26 residues within 4Å: Chain A: T.6, P.7, I.9, T.24, D.27, F.29, R.33, G.34, K.35, R.36, V.37, F.65 Chain B: D.27, F.29, S.31, I.32, R.33, G.34, K.35, R.36, F.65 Chain C: T.67, R.68 Chain D: F.29 Ligands: QJE.3, 1PE.5 30 PLIP interactions: 17 interactions with chain A, 10 interactions with chain B, 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:I.9, A:R.33, A:R.33, A:R.36, A:V.37, A:F.65, A:F.65, B:I.32, B:R.33, B:R.33, B:R.36, D:F.29, D:F.29 Hydrogen bonds: A:R.33, A:K.35, A:R.36, A:R.36, A:V.37, B:D.27, B:I.32, B:R.33, B:K.35, C:R.68 Water bridges: A:K.35, A:R.36, A:V.37, B:K.35, B:R.36 Salt bridges: A:R.36 pi-Cation interactions: A:R.33 TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.2: 26 residues within 4Å: Chain A: T.67, R.68 Chain B: F.29 Chain C: T.6, P.7, I.9, T.24, D.27, F.29, R.33, G.34, K.35, R.36, V.37, F.65 Chain D: D.27, F.29, S.31, I.32, R.33, G.34, K.35, R.36, F.65 Ligands: QJE.4, 1PE.5 32 PLIP interactions: 20 interactions with chain C, 9 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:I.9, C:R.33, C:R.33, C:R.36, C:V.37, C:F.65, C:F.65, D:I.32, D:R.33, D:R.33, D:R.36, B:F.29, B:F.29 Hydrogen bonds: C:D.27, C:R.33, C:R.33, C:K.35, C:R.36, C:R.36, C:V.37, D:I.32, D:R.33, D:K.35, A:R.68 Water bridges: C:R.33, C:K.35, C:R.36, C:V.37, D:R.33, D:K.35 Salt bridges: C:R.36 pi-Cation interactions: C:R.33

2 x QJE: 3-[2-[2-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]propan-1-ol(Non-covalent)

QJE.3: 3 residues within 4Å: Chain B: R.36, V.37 Ligands: TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.37 QJE.4: 3 residues within 4Å: Chain D: R.36, V.37 Ligands: TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.37

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

1PE.5: 13 residues within 4Å: Chain A: F.65 Chain B: F.29, I.32 Chain C: V.37, F.65 Chain D: F.29, I.32 Ligands: TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.1, TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.1, TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.1, TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.2, TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.2, TYR-MET-TRP-ASP-GLY-TRP-TYR-MET.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynagh, T. et al., Peptide Inhibitors of the alpha-Cobratoxin-Nicotinic Acetylcholine Receptor Interaction. J.Med.Chem. (2020)

Release Date

2020-12-02

Peptides

Alpha-cobratoxin: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Alpha-cobratoxin

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