2JF0 | pdb_00002jf0

Mus musculus acetylcholinesterase in complex with tabun and Ortho-7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.251 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Novel Nerve-Agent Antidote Design Based on Crystallographic and Mass Spectrometric Analyses of Tabun-Conjugated Acetylcholinesterase in Complex with Antidotes.

Ekstrom, F.J.Astot, C.Pang, Y.

(2007) Clin Pharmacol Ther 82: 282

  • DOI: https://doi.org/10.1038/sj.clpt.6100151
  • Primary Citation Related Structures: 
    2JEY, 2JEZ, 2JF0

  • PubMed Abstract: 

    Organophosphorus compound-based nerve agents inhibit the essential enzyme acetylcholinesterase (AChE) causing acute toxicity and death. Clinical treatment of nerve-agent poisoning is to use oxime-based antidotes to reactivate the inhibited AChE. However, the nerve agent tabun is resistant to oximes. To design improved oximes, crystal structures of a tabun-conjugated AChE in complex with different oximes are needed to guide the structural modifications of known antidotes. However, this type of structure is extremely challenging to obtain because both deamidation of the tabun conjugate and reactivation of AChE occur during crystallographic experiments. Here we report, for the first time, the crystal structures of Ortho-7 and HLö-7 in complex with AChE that is conjugated to an intact tabun. These structures were determined by our new strategy of combining crystallographic and mass spectrometric analyses of AChE crystals. The results explain the relative reactivation potencies of the two oximes and offer insights into improving known medical antidotes.


  • Organizational Affiliation
    • FOI CBRN Defence and Security, Umeå, Sweden. fredrik.ekstrom@foi.se

Macromolecule Content 

  • Total Structure Weight: 121.71 kDa 
  • Atom Count: 8,658 
  • Modeled Residue Count: 1,069 
  • Deposited Residue Count: 1,096 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACETYLCHOLINESTERASE
A, B
548Mus musculusMutation(s): 0 
EC: 3.1.1.7 (PDB Primary Data), 3.1.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus)
Explore P21836 
Go to UniProtKB:  P21836
IMPC:  MGI:87876
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SUN
Query on SUN
A, B
L-PEPTIDE LINKINGC7 H17 N2 O5 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.73α = 90
b = 108.58β = 90
c = 220.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2021-05-12
    Changes: Derived calculations, Other
  • Version 1.5: 2023-12-13
    Changes: Data collection, Database references, Refinement description