1JJB

A neutral molecule in cation-binding site: Specific binding of PEG-SH to Acetylcholinesterase from Torpedo californica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A neutral molecule in a cation-binding site: specific binding of a PEG-SH to acetylcholinesterase from Torpedo californica.

Koellner, G.Steiner, T.Millard, C.B.Silman, I.Sussman, J.L.

(2002) J.Mol.Biol. 320: 721-725


  • PubMed Abstract: 
  • The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an unt ...

    The crystal structure of acetylcholinesterase from Torpedo californica complexed with the uncharged inhibitor, PEG-SH-350 (containing mainly heptameric polyethylene glycol with a terminal thiol group) is determined at 2.3 A resolution. This is an untypical acetylcholinesterase inhibitor, since it lacks the cationic moiety typical of the substrate (acetylcholine). In the crystal structure, the elongated ligand extends along the whole of the deep and narrow active-site gorge, with the terminal thiol group bound near the bottom, close to the catalytic site. Unexpectedly, the cation-binding site (formed by the faces of aromatic side-chains) is occupied by CH(2) groups of the inhibitor, which are engaged in C-H...pi interactions that structurally mimic the cation-pi interactions made by the choline moiety of acetylcholine. In addition, the PEG-SH molecule makes numerous other weak but specific interactions of the C-H...O and C-H...pi types.


    Organizational Affiliation

    Institut für Chemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany. koellner@chemie.fu-berlin.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINESTERASE
A
532Torpedo californicaGene Names: ache
EC: 3.1.1.7
Find proteins for P04058 (Torpedo californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PE7
Query on PE7

Download SDF File 
Download CCD File 
A
1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL
C14 H30 O7 S
ACMBXVJDKVNCGH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.200α = 90.00
b = 111.200β = 90.00
c = 137.119γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance