Experimental Data Snapshot

  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history


X-Ray Structures of Torpedo Californica Acetylcholinesterase Complexed with (+)-Huperzine a and (-)-Huperzine B: Structural Evidence for an Active Site Rearrangement

Dvir, H.Jiang, H.L.Wong, D.M.Harel, M.Chetrit, M.He, X.C.Jin, G.Y.Yu, G.L.Tang, X.C.Silman, I.Bai, D.L.Sussman, J.L.

(2002) Biochemistry 41: 10810

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinetic and structural data are presented on the interaction with Torpedo californica acetylcholinesterase (TcAChE) of (+)-huperzine A, a synthetic enantiomer of the anti-Alzheimer drug, (-)-huperzine A, and of its natural homologue (-)-huperzine B. ...

    Kinetic and structural data are presented on the interaction with Torpedo californica acetylcholinesterase (TcAChE) of (+)-huperzine A, a synthetic enantiomer of the anti-Alzheimer drug, (-)-huperzine A, and of its natural homologue (-)-huperzine B. (+)-Huperzine A and (-)-huperzine B bind to the enzyme with dissociation constants of 4.30 and 0.33 microM, respectively, compared to 0.18 microM for (-)-huperzine A. The X-ray structures of the complexes of (+)-huperzine A and (-)-huperzine B with TcAChE were determined to 2.1 and 2.35 A resolution, respectively, and compared to the previously determined structure of the (-)-huperzine A complex. All three interact with the "anionic" subsite of the active site, primarily through pi-pi stacking and through van der Waals or C-H.pi interactions with Trp84 and Phe330. Since their alpha-pyridone moieties are responsible for their key interactions with the active site via hydrogen bonding, and possibly via C-H.pi interactions, all three maintain similar positions and orientations with respect to it. The carbonyl oxygens of all three appear to repel the carbonyl oxygen of Gly117, thus causing the peptide bond between Gly117 and Gly118 to undergo a peptide flip. As a consequence, the position of the main chain nitrogen of Gly118 in the "oxyanion" hole in the native enzyme becomes occupied by the carbonyl of Gly117. Furthermore, the flipped conformation is stabilized by hydrogen bonding of Gly117O to Gly119N and Ala201N, the other two functional elements of the three-pronged "oxyanion hole" characteristic of cholinesterases. All three inhibitors thus would be expected to abolish hydrolysis of all ester substrates, whether charged or neutral.

    Related Citations: 
    • Atomic Structure of Acetylcholinesterase from Torpedo Californica: A Prototypic Acetylcholine-Binding Protein
      Sussman, J.L.,Harel, M.,Frolow, F.,Oefner, C.,Goldman, A.,Toker, L.,Silman, I.
      (1991) Science 253: 872
    • Structure and Dynamics of the Active Site Gorge of Acetylcholinesterase: Synergistic Use of Molecular Dynamics Simulation and X-Ray Crystallography
      Axelsen, P.H.,Harel, M.,Silman, I.,Sussman, J.L.
      (1994) Protein Sci. 3: 188
    • Residues in Torpedo Californica Acetylcholinesterase Necessary for Processing to a Glycosyl Phosphatidylinositol-Anchored Form
      Bucht, G.,Hjalmarsson, K.
      (1996) Biochim.Biophys.Acta 1292: 223
    • Primary Structure of Torpedo Californica Acetylcholinesterase Deduced from its Cdna Sequence
      Schumacher, M.,Camp, S.,Maulet, Y.,Newton, M.,Macphee-Quigley, K.,Taylor, S.S.,Friedmann, T.,Taylor, P.
      (1986) Nature 319: 407
    • Quaternary Ligand Binding to Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase
      Harel, M.,Schalk, I.,Ehret-Sabatier, L.,Bouet, F.,Goeldner, M.,Hirth, C.,Axelsen, P.H.,Silman, I.,Sussman, J.L.
      (1993) Proc.Natl.Acad.Sci.USA 90: 9031
    • Purification and Crystallization of a Dimeric Form of Acetylcholinesterase from Torpedo Californica Subsequent to Solubilization with Phosphatidylinositol-Specific Phospholipase C
      Sussman, J.L.,Harel, M.,Frolow, F.,Varon, L.,Toker, L.,Futerman, A.H.,Silman, I.
      (1988) J.Mol.Biol. 203: 821

    Organizational Affiliation

    Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.


Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
537Tetronarce californicaMutation(s): 0 
Gene Names: ache
Find proteins for P04058 (Tetronarce californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download SDF File 
Download CCD File 
C8 H15 N O6
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Resolution: 1.8 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.185 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.573α = 90.00
b = 111.573β = 90.00
c = 137.587γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-08
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 2.0: 2019-04-03
    Type: Atomic model, Data collection, Derived calculations, Experimental preparation, Other