1VOT | pdb_00001vot

ACETYLCHOLINESTERASE (E.C. 3.1.1.7) COMPLEXED WITH HUPERZINE A

• PDB DOI: https://doi.org/10.2210/pdb1VOT/pdb

• Classification: HYDROLASE
• Organism(s): Tetronarce californica
• Mutation(s): No 


• Deposited: 1996-06-23 Released: 1997-06-16 
• Deposition Author(s): Raves, M.L., Harel, M., Silman, I., Sussman, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.248 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structure of acetylcholinesterase complexed with the nootropic alkaloid, (-)-huperzine A.

Raves, M.L., Harel, M., Pang, Y.P., Silman, I., Kozikowski, A.P., Sussman, J.L.

(1997) Nat Struct Biol 4: 57-63

• PubMed: 8989325 
• DOI: https://doi.org/10.1038/nsb0197-57
• Primary Citation Related Structures: 
  1VOT, 2ACE


• PubMed Abstract: 
  

  (-)-Huperzine A (HupA) is found in an extract from a club moss that has been used for centuries in Chinese folk medicine. Its action has been attributed to its ability to strongly inhibit acetylcholinesterase (AChE). The crystal structure of the complex of AChE with optically pure HupA at 2.5 A resolution shows an unexpected orientation for the inhibitor with surprisingly few strong direct interactions with protein residues to explain its high affinity. This structure is compared to the native structure of AChE devoid of any inhibitor as determined to the same resolution. An analysis of the affinities of structural analogues of HupA, correlated with their interactions with the protein, shows the importance of individual hydrophobic interactions between HupA and aromatic residues in the active-site gorge of AChE.

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Organizational Affiliation: 
• Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 60.98 kDa 
• Atom Count: 4,366 
• Modeled Residue Count: 529 
• Deposited Residue Count: 537 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINESTERASE	A	537	Tetronarce californica	Mutation(s): 0  EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HUP	B [auth A]	Huperzine A C15 H18 N2 O ZRJBHWIHUMBLCN-YQEJDHNASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HUP	BindingDB:  1VOT	IC50: 11.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.248 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.632	α = 90
b = 112.632	β = 90
c = 136.378	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-06-16 
Deposition Author(s): Raves, M.L., Harel, M., Silman, I., Sussman, J.L.

Revision History  

• Version 1.0: 1997-06-16
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2013-10-23
  Changes: Non-polymer description
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary