1N5R

Crystal structure of the mouse acetylcholinesterase-propidium complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report



Literature

Structural insights into ligand interactions at the acetylcholinesterase peripheral anionic site

Bourne, Y., Taylor, P., Radic, Z., Marchot, P.

(2003) EMBO J 22: 1-12

  • DOI: 10.1093/emboj/cdg005
  • Primary Citation of Related Structures:  
    1KU6, 1N5M, 1N5R, 1J06, 1J07

  • PubMed Abstract: 

    • The peripheral anionic site on acetylcholinesterase (AChE), located at the active center gorge entry, encompasses overlapping binding sites for allosteric activators and inhibitors; yet, the molecular mechanisms coupling this site to the active cente ...

    The peripheral anionic site on acetylcholinesterase (AChE), located at the active center gorge entry, encompasses overlapping binding sites for allosteric activators and inhibitors; yet, the molecular mechanisms coupling this site to the active center at the gorge base to modulate catalysis remain unclear. The peripheral site has also been proposed to be involved in heterologous protein associations occurring during synaptogenesis or upon neurodegeneration. A novel crystal form of mouse AChE, combined with spectrophotometric analyses of the crystals, enabled us to solve unique structures of AChE with a free peripheral site, and as three complexes with peripheral site inhibitors: the phenylphenanthridinium ligands, decidium and propidium, and the pyrogallol ligand, gallamine, at 2.20-2.35 A resolution. Comparison with structures of AChE complexes with the peptide fasciculin or with organic bifunctional inhibitors unveils new structural determinants contributing to ligand interactions at the peripheral site, and permits a detailed topographic delineation of this site. Hence, these structures provide templates for designing compounds directed to the enzyme surface that modulate specific surface interactions controlling catalytic activity and non-catalytic heterologous protein associations.

    Organizational Affiliation: 

    Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 6098, Marseille, France. yves@afmb.cnrs-mrs.fr



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
acetylcholinesteraseA, B543Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
NIH Common Fund Data Resources
IMPC  MGI:87876
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PRM
Query on PRM
Download CCD File 
A
3,8-DIAMINO-5[3-(DIETHYLMETHYLAMMONIO)PROPYL]-6-PHENYLPHENANTHRIDINIUM
C27 H34 N4
ZDWVWKDAWBGPDN-UHFFFAOYSA-O		 Ligand Interaction
P6G
Query on P6G
Download CCD File 
A
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
PG4
Query on PG4
Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PRMKi :  2200   nM  PDBBind
PRMKi:  2200   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.552α = 90
b = 111.665β = 90
c = 226.834γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary