6NTN | pdb_00006ntn

Crystal Structure of Recombinant Human Acetylcholinesterase Inhibited by A-230 in Complex with the Reactivator, HI-6

• PDB DOI: https://doi.org/10.2210/pdb6NTN/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: 2.70 Å
• R-Value Free: 
  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (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: 121.79 kDa 
• Atom Count: 8,899 
• 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: 2		Go to GlyGen: P22303-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HI6	F [auth A], H [auth B]	4-(AMINOCARBONYL)-1-[({2-[(E)-(HYDROXYIMINO)METHYL]PYRIDINIUM-1-YL}METHOXY)METHYL]PYRIDINIUM C14 H16 N4 O3 FJZDLOMCEPUCII-UHFFFAOYSA-P
NAG	I [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
L2Y	G [auth A], J [auth B]	(S)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidic fluoride C7 H16 F N2 O P OUJDIWHRYQBZSR-CRALRDPISA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HI6	BindingDB:  6NTN	Kd: min: 1.50e+4, max: 2.34e+5 (nM) from 6 assay(s)
		IC50: min: 6.36e+5, max: 1.36e+6 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.215 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.402	α = 90
b = 104.402	β = 90
c = 323.683	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: 2024-10-09
  Changes: Structure summary