2CEK | pdb_00002cek

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.206 (Depositor), 0.218 (DCC)
R-Value Work:
0.175 (Depositor), 0.185 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed
DOI: https://doi.org/10.1021/ja058683b
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04058
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N8T Query on N8T Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.206 (Depositor), 0.218 (DCC)
R-Value Work: 0.175 (Depositor), 0.185 (DCC)
R-Value Observed: 0.175 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2006-04-10

Deposition Author(s):

Revision History (Full details and data files)

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