2J3D | pdb_00002j3d

Native monoclinic form of Torpedo acetylcholinesterase

• PDB DOI: https://doi.org/10.2210/pdb2J3D/pdb

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


• Deposited: 2006-08-20 Released: 2008-06-24 
• Deposition Author(s): Harel, M., Sussman, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.261 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Native Monoclinic Form of Torpedo Acetylcholinesterase

Harel, M., Sussman, J.L.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 62.11 kDa 
• Atom Count: 4,390 
• Modeled Residue Count: 533 
• 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
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.261 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.74	α = 90
b = 105.49	β = 106.62
c = 70.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Harel, M., Sussman, J.L.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-12
  Changes: Advisory, Derived calculations
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.6: 2024-11-13
  Changes: Structure summary