Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
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: 9133 
• Modelled Residue Count: 1063 
• Deposited Residue Count: 1084 
• Unique protein chains: 1

5HF9

Crystal structure of human acetylcholinesterase in complex with paraoxon and HI6

• PDB DOI: 10.2210/pdb5HF9/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-01-06 Released: 2016-06-22 
• Deposition Author(s): Franklin, M.F., Rudolph, M.J., Ginter, C., Cassidy, M.S., Cheung, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Structures of paraoxon-inhibited human acetylcholinesterase reveal perturbations of the acyl loop and the dimer interface.

Franklin, M.C., Rudolph, M.J., Ginter, C., Cassidy, M.S., Cheung, J.

(2016) Proteins 84: 1246-1256

• PubMed: 27191504 
• DOI: 10.1002/prot.25073
• Primary Citation of Related Structures:  
  5HF5, 5HF6, 5HF8, 5HF9, 5HFA


• PubMed Abstract: 
  

Irreversible inhibition of the essential nervous system enzyme acetylcholinesterase by organophosphate nerve agents and pesticides may quickly lead to death. Oxime reactivators currently used as antidotes are generally less effective against pesticide exposure than nerve agent exposure, and pesticide exposure constitutes the majority of cases of organophosphate poisoning in the world. The current lack of published structural data specific to human acetylcholinesterase organophosphate-inhibited and oxime-bound states hinders development of effective medical treatments. We have solved structures of human acetylcholinesterase in different states in complex with the organophosphate insecticide, paraoxon, and oximes. Reaction with paraoxon results in a highly perturbed acyl loop that causes a narrowing of the gorge in the peripheral site that may impede entry of reactivators. This appears characteristic of acetylcholinesterase inhibition by organophosphate insecticides but not nerve agents. Additional changes seen at the dimer interface are novel and provide further examples of the disruptive effect of paraoxon. Ternary structures of paraoxon-inhibited human acetylcholinesterase in complex with the oximes HI6 and 2-PAM reveals relatively poor positioning for reactivation. This study provides a structural foundation for improved reactivator design for the treatment of organophosphate intoxication. Proteins 2016; 84:1246-1256. © 2016 Wiley Periodicals, Inc.

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Organizational Affiliation: 

Special Projects Group, New York Structural Biology Center, New York, New York, 10027.

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

Oligosaccharides

Help

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE8	K [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C16 H34 O9 GLZWNFNQMJAZGY-UHFFFAOYSA-N
HI6	H [auth A], O [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
DEP	E [auth A], J [auth B]	DIETHYL PHOSPHONATE C4 H11 O3 P MJUJXFBTEFXVKU-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	N [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HI6	BindingDB:  5HF9	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: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.931	α = 90
b = 105.931	β = 90
c = 324.415	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-01-06 
• Released Date: 2016-06-22 
Deposition Author(s): Franklin, M.F., Rudolph, M.J., Ginter, C., Cassidy, M.S., Cheung, J.

Revision History  

• Version 1.0: 2016-06-22
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary