4BFQ

Assembly of a triple pi-stack of ligands in the binding site of Aplysia californica acetylcholine binding protein (AChBP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Assembly of a Pi-Pi Stack of Ligands in the Binding Site of an Acetylcholine Binding Protein

Stornaiuolo, M.De Kloe, G.E.Rucktooa, P.Fish, A.van Elk, R.Edink, E.S.Bertrand, D.Smit, A.B.de Esch, I.J.P.Sixma, T.K.

(2013) Nat.Commun. 4: 1875

  • DOI: 10.1038/ncomms2900

  • PubMed Abstract: 
  • Acetylcholine-binding protein is a water-soluble homologue of the extracellular ligand-binding domain of cys-loop receptors. It is used as a structurally accessible prototype for studying ligand binding to these pharmaceutically important pentameric ...

    Acetylcholine-binding protein is a water-soluble homologue of the extracellular ligand-binding domain of cys-loop receptors. It is used as a structurally accessible prototype for studying ligand binding to these pharmaceutically important pentameric ion channels, in particular to nicotinic acetylcholine receptors, due to conserved binding site residues present at the interface between two subunits. Here we report that an aromatic conjugated small molecule binds acetylcholine-binding protein in an ordered π-π stack of three identical molecules per binding site, two parallel and one antiparallel. Acetylcholine-binding protein stabilizes the assembly of the stack by aromatic contacts. Thanks to the plasticity of its ligand-binding site, acetylcholine-binding protein can accommodate the formation of aromatic stacks of different size by simple loop repositioning and minimal adjustment of the interactions. This type of supramolecular binding provides a novel paradigm in drug design.


    Organizational Affiliation

    Division of Biochemistry and Center for Biomedical Genetics, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOLUBLE ACETYLCHOLINE RECEPTOR
A, B, C, D, E
217Aplysia californicaN/A
Find proteins for Q8WSF8 (Aplysia californica)
Go to UniProtKB:  Q8WSF8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
083
Query on 083

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Download CCD File 
A, B, C, D, E
4,6-dimethyl-N'-(3-pyridin-2-ylisoquinolin-1-yl)pyrimidine-2-carboximidamide
C21 H18 N6
YKSJLEVXPOMXPZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.730α = 90.00
b = 78.330β = 102.67
c = 106.530γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2017-12-20
    Type: Database references, Structure summary