5NAU

Torpedo californica acetylcholinesterase in complex with a non-chiral donepezil-like compound 20

• PDB DOI: https://doi.org/10.2210/pdb5NAU/pdb

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


• Deposited: 2017-02-28 Released: 2018-05-02 
• Deposition Author(s): Caliandro, R., Pesaresi, A., Lamba, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 63.54 kDa 
• Atom Count: 4,634 
• Modelled Residue Count: 532 
• Deposited Residue Count: 543 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A	543	Tetronarce californica	Mutation(s): 0  EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DZ0	E [auth A]	(2~{E})-5-methoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one C23 H25 N O2 CNIWTTNRVIMZIP-DEDYPNTBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DZ0	Binding MOAD:  5NAU	Ki: 29.86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.62	α = 90
b = 111.62	β = 90
c = 136.71	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Caliandro, R., Pesaresi, A., Lamba, D.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary