Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 121.35 kDa 
• Atom Count: 8890 
• Modelled Residue Count: 1070 
• Deposited Residue Count: 1086 
• Unique protein chains: 1

1N5R

Crystal structure of the mouse acetylcholinesterase-propidium complex

• PDB DOI: 10.2210/pdb1N5R/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2002-11-07 Released: 2003-02-04 
• Deposition Author(s): Bourne, Y., Taylor, P., Radic, Z., Marchot, P.

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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 

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

• PubMed: 12505979 
• DOI: 10.1093/emboj/cdg005
• Primary Citation of Related Structures:  
  1J06, 1J07, 1KU6, 1N5M, 1N5R


• 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 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.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, CNRS UMR 6098, Marseille, France. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
acetylcholinesterase	A, B	543	Mus musculus	Mutation(s): 0  Gene Names: Ache EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus) Explore P21836  Go to UniProtKB:  P21836
IMPC:  MGI:87876

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRM	F [auth A]	3,8-DIAMINO-5[3-(DIETHYLMETHYLAMMONIO)PROPYL]-6-PHENYLPHENANTHRIDINIUM C27 H34 N4 ZDWVWKDAWBGPDN-UHFFFAOYSA-O
P6G	E [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
NAG	D [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	I [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ACY	G [auth A], J [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PRM	Binding MOAD:  1N5R	Ki: 2200 (nM) from 1 assay(s)
	PDBBind:  1N5R	Ki: 2200 (nM) from 1 assay(s)

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 = 79.552	α = 90
b = 111.665	β = 90
c = 226.834	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-11-07 
• Released Date: 2003-02-04 
Deposition Author(s): Bourne, Y., Taylor, P., Radic, Z., Marchot, P.

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