6NTL | pdb_00006ntl

Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-234

• PDB DOI: https://doi.org/10.2210/pdb6NTL/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-01-29 Released: 2020-07-01 
• Deposition Author(s): Bester, S.M., Guelta, M.A., Height, J.J., Pegan, S.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Insights into inhibition of human acetylcholinesterase by Novichok, A-series Nerve Agents

Height, J.J., Bester, S.M., Guelta, M.A., Bae, S.Y., Cheung, J., Pegan, S.D.

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: 121.33 kDa 
• Atom Count: 9,495 
• Modeled Residue Count: 1,061 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	542	Homo sapiens	Mutation(s): 0  Gene Names: ACHE EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P22303 (Homo sapiens) Explore P22303  Go to UniProtKB:  P22303
PHAROS:  P22303 GTEx:  ENSG00000087085
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P22303-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7PE	F [auth A]	2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL C14 H30 O7 UKXKPKBTMYNOFS-UHFFFAOYSA-N
L1M	G [auth A], H [auth B]	ethyl (R)-N-[(1E)-1-(diethylamino)ethylidene]phosphonamidate C8 H19 N2 O2 P OJNAFPOCQGTUIK-CMDGGOBGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.966	α = 90
b = 104.966	β = 90
c = 323.844	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Bester, S.M., Guelta, M.A., Height, J.J., Pegan, S.D.

Revision History  

• Version 1.0: 2020-07-01
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary