5E2I

Acetylcholinesterase Methylene Blue no PEG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex.

Dym, O.Song, W.Felder, C.Roth, E.Shnyrov, V.Ashani, Y.Xu, Y.Joosten, R.P.Weiner, L.Sussman, J.L.Silman, I.

(2016) Protein Sci. 25: 1096-1114

  • DOI: 10.1002/pro.2923
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presenc ...

    Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presence of individual ethyleneglycol oligomers. We report a case in which ethyleneglycol oligomers' presence in a crystal structure markedly affected the bound ligand's position. Specifically, we compared the positions of methylene blue and decamethonium in acetylcholinesterase complexes obtained using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The ligands' positions within the active-site gorge in complexes obtained using PEG200 are influenced by presence of ethyleneglycol oligomers in both cases bound to W84 at the gorge's bottom, preventing interaction of the ligand's proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å further up the gorge than in complexes obtained using crystals precipitated with ammonium sulfate, in which the quaternary groups make direct π-cation interactions with the indole. These findings have implications for structure-based drug design, since data for ligand-protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design.


    Organizational Affiliation

    Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholinesterase
A
532Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
Find proteins for P04058 (Tetronarce californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DME
Query on DME

Download SDF File 
Download CCD File 
A
DECAMETHONIUM ION
C16 H38 N2
MTCUAOILFDZKCO-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DMEIC50: 1063 nM (97) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.609α = 90.00
b = 112.609β = 90.00
c = 136.871γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASESphasing
HKL-2000data reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-01 
  • Released Date: 2016-03-30 
  • Deposition Author(s): Dym, O.

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references
  • Version 1.2: 2019-04-10
    Type: Data collection, Structure summary