2WHP

Crystal structure of acetylcholinesterase, phosphonylated by sarin and in complex with HI-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Hi-6Sarin-Acetylcholinesterase Determined by X-Ray Crystallography and Molecular Dynamics Simulation: Reactivator Mechanism and Design.

Ekstrom, F.Hornberg, A.Artursson, E.Hammarstrom, L.G.Schneider, G.Pang, Y.P.

(2009) PLoS One 4: E5957

  • DOI: 10.1371/journal.pone.0005957
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Organophosphonates such as isopropyl metylphosphonofluoridate (sarin) are extremely toxic as they phosphonylate the catalytic serine residue of acetylcholinesterase (AChE), an enzyme essential to humans and other species. Design of effective AChE rea ...

    Organophosphonates such as isopropyl metylphosphonofluoridate (sarin) are extremely toxic as they phosphonylate the catalytic serine residue of acetylcholinesterase (AChE), an enzyme essential to humans and other species. Design of effective AChE reactivators as antidotes to various organophosphonates requires information on how the reactivators interact with the phosphonylated AChEs. However, such information has not been available hitherto because of three main challenges. First, reactivators are generally flexible in order to change from the ground state to the transition state for reactivation; this flexibility discourages determination of crystal structures of AChE in complex with effective reactivators that are intrinsically disordered. Second, reactivation occurs upon binding of a reactivator to the phosphonylated AChE. Third, the phosphorous conjugate can develop resistance to reactivation. We have identified crystallographic conditions that led to the determination of a crystal structure of the sarin(nonaged)-conjugated mouse AChE in complex with [(E)-[1-[(4-carbamoylpyridin-1-ium-1-yl)methoxymethyl]pyridin-2-ylidene]methyl]-oxoazanium dichloride (HI-6) at a resolution of 2.2 A. In this structure, the carboxyamino-pyridinium ring of HI-6 is sandwiched by Tyr124 and Trp286, however, the oxime-pyridinium ring is disordered. By combining crystallography with microsecond molecular dynamics simulation, we determined the oxime-pyridinium ring structure, which shows that the oxime group of HI-6 can form a hydrogen-bond network to the sarin isopropyl ether oxygen, and a water molecule is able to form a hydrogen bond to the catalytic histidine residue and subsequently deprotonates the oxime for reactivation. These results offer insights into the reactivation mechanism of HI-6 and design of better reactivators.


    Organizational Affiliation

    Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden. fredrik.ekstrom@foi.se



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINESTERASE
A
548Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
Find proteins for P21836 (Mus musculus)
Go to UniProtKB:  P21836
NIH Common Fund Data Resources
IMPC  MGI:87876

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACETYLCHOLINESTERASE
B
548Mus musculusMutation(s): 0 
Gene Names: Ache
EC: 3.1.1.7
Find proteins for P21836 (Mus musculus)
Go to UniProtKB:  P21836
NIH Common Fund Data Resources
IMPC  MGI:87876
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HI6
Query on HI6

Download CCD File 
A, B
4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM
C14 H16 N4 O3
FJZDLOMCEPUCII-UHFFFAOYSA-P
 Ligand Interaction
P6G
Query on P6G

Download CCD File 
B
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SGB
Query on SGB
AL-PEPTIDE LINKINGC7 H16 N O5 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HI6Kd:  100000   nM  Binding MOAD
HI6Kd:  27000   nM  BindingDB
HI6Kd:  15000   nM  BindingDB
HI6Kd:  234000   nM  BindingDB
HI6Kd :  100000   nM  PDBBind
HI6IC50:  667800   nM  BindingDB
HI6IC50:  1360000   nM  BindingDB
HI6Kd:  93000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.26α = 90
b = 112.15β = 90
c = 226.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    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