X-ray structure of human acetylcholinesterase ternary complex with paraoxon and oxime MMB4 (POX-hAChE-MMB4)

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering.

Gerlits, O.Fajer, M.Cheng, X.Blumenthal, D.K.Radic, Z.Kovalevsky, A.

(2022) Structure 30: 1538-1549.e3

  • DOI: https://doi.org/10.1016/j.str.2022.09.006
  • Primary Citation of Related Structures:  
    8DT2, 8DT4, 8DT5, 8DT7

  • PubMed Abstract: 

    Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50 cm -1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

  • Organizational Affiliation

    Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
550Homo sapiensMutation(s): 0 
Gene Names: ACHE
UniProt & NIH Common Fund Data Resources
Find proteins for P22303 (Homo sapiens)
Explore P22303 
Go to UniProtKB:  P22303
PHAROS:  P22303
GTEx:  ENSG00000087085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22303
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3VI (Subject of Investigation/LOI)
Query on 3VI

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
C13 H14 N4 O2
DEP (Subject of Investigation/LOI)
Query on DEP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
C4 H11 O3 P
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.503α = 90
b = 124.503β = 90
c = 129.093γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesU01NS083451

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description