2CEK

Conformational Flexibility in the Peripheral Site of Torpedo californica Acetylcholinesterase Revealed by the Complex Structure with a Bifunctional Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2CEK/pdb

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


• Deposited: 2006-02-08 Released: 2006-04-10 
• Deposition Author(s): Sanson, B., Colletier, J.P., Nachon, F., Gabellieri, E., Fattorusso, C., Campiani, G., Weik, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.206 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Conformational flexibility in the peripheral site of Torpedo californica acetylcholinesterase revealed by the complex structure with a bifunctional inhibitor.

Colletier, J.P., Sanson, B., Nachon, F., Gabellieri, E., Fattorusso, C., Campiani, G., Weik, M.

(2006) J Am Chem Soc 128: 4526-4527

• PubMed: 16594661 
• DOI: https://doi.org/10.1021/ja058683b
• Primary Citation of Related Structures:  
  2CEK


• PubMed Abstract: 
  

  The X-ray crystallographic structure of Torpedo californica acetylcholinesterase (TcAChE) in complex with the bifunctional inhibitor NF595, a potentially new anti-Alzheimer drug, has been solved. For the first time in TcAChE, a major conformational change in the peripheral-site tryptophan residue is observed upon complexation. The observed conformational flexibility highlights the dynamic nature of protein structures and is of importance for structure-based drug design.

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Organizational Affiliation: 

Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale, 38027 Grenoble, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.94 kDa 
• Atom Count: 5,162 
• Modelled Residue Count: 532 
• Deposited Residue Count: 535 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACETYLCHOLINESTERASE	A	535	Tetronarce californica	Mutation(s): 0  EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N8T	E [auth A]	N-[8-(1,2,3,4-TETRAHYDROACRIDIN-9-YLTHIO)OCTYL]-1,2,3,4-TETRAHYDROACRIDIN-9-AMINE C34 H41 N3 S COEYCPFFRLYNSC-UHFFFAOYSA-N
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	F [auth A], G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE	H [auth A], I [auth A], J [auth A], K [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.206 
• R-Value Work: 0.175 
• R-Value Observed: 0.175 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.94	α = 90
b = 111.94	β = 90
c = 137.12	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-10 
Deposition Author(s): Sanson, B., Colletier, J.P., Nachon, F., Gabellieri, E., Fattorusso, C., Campiani, G., Weik, M.

Revision History  

• Version 1.0: 2006-04-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2018-07-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 3.1: 2021-05-12
  Changes: Derived calculations, Structure summary
• Version 3.2: 2023-12-13
  Changes: Data collection, Database references, Refinement description
• Version 3.3: 2024-10-16
  Changes: Structure summary