Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.33 kDa 
• Atom Count: 4438 
• Modelled Residue Count: 526 
• Deposited Residue Count: 529 
• Unique protein chains: 1

6T9S

Human Butyrylcholinesterase in complex with 2-(N-hydroxyimino)-N-[(1S)-3-{4-[(2-methyl-1H-imidazol-1-yl)methyl]-1H-1,2,3-triazol-1-yl}-1- phenylpropyl]acetamide

• PDB DOI: 10.2210/pdb6T9S/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2019-10-28 Released: 2020-07-15 
• Deposition Author(s): Brazzolotto, X., Sinko, G., Marakovic, N., Knezevic, A.
• Funding Organization(s): French Ministry of Armed Forces

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.209 

Literature

Enantioseparation, in vitro testing, and structural characterization of triple-binding reactivators of organophosphate-inhibited cholinesterases.

Marakovic, N., Knezevic, A., Roncevic, I., Brazzolotto, X., Kovarik, Z., Sinko, G.

(2020) Biochem J 477: 2771-2790

• PubMed: 32639532 
• DOI: 10.1042/BCJ20200192
• Primary Citation of Related Structures:  
  6T9P, 6T9S


• PubMed Abstract: 
  

The enantiomers of racemic 2-hydroxyimino-N-(azidophenylpropyl)acetamide-derived triple-binding oxime reactivators were separated, and tested for inhibition and reactivation of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibited with tabun (GA), cyclosarin (GF), sarin (GB), and VX. Both enzymes showed the greatest affinity toward the methylimidazole derivative (III) of 2-hydroxyimino-N-(azidophenylpropyl)acetamide (I). The crystal structure was determined for the complex of oxime III within human BChE, confirming that all three binding groups interacted with active site residues. In the case of BChE inhibited by GF, oximes I (kr = 207 M-1 min-1) and III (kr = 213 M-1 min-1) showed better reactivation efficiency than the reference oxime 2-PAM. Finally, the key mechanistic steps in the reactivation of GF-inhibited BChE with oxime III were modeled using the PM7R6 method, stressing the importance of proton transfer from Nε of His438 to Oγ of Ser203 for achieving successful reactivation.

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Organizational Affiliation: 

Biochemistry and Organic Analytical Chemistry Unit, Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10 000 Zagreb, Croatia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A	529	Homo sapiens	Mutation(s): 4  Gene Names: BCHE, CHE1 EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens) Explore P06276  Go to UniProtKB:  P06276
PHAROS:  P06276 GTEx:  ENSG00000114200

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(5-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3	N/A	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MXK (Subject of Investigation/LOI)	I [auth A]	(2~{E})-2-hydroxyimino-~{N}-[(1~{S})-3-[4-[(2-methylimidazol-1-yl)methyl]-1,2,3-triazol-1-yl]-1-phenyl-propyl]ethanamid e C18 H21 N7 O2 ZMAXDRHDDCRKQC-PBGVMVHZSA-N
NAG	F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	J [auth A], K [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.209 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.14	α = 90
b = 154.14	β = 90
c = 127.52	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-10-28 
• Released Date: 2020-07-15 
Deposition Author(s): Brazzolotto, X., Sinko, G., Marakovic, N., Knezevic, A.

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Funding Organization	Location	Grant Number
French Ministry of Armed Forces	France	NBC-5-C-4210

Revision History  

• Version 1.0: 2020-07-15
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-08-19
  Changes: Database references