7KY2 | pdb_00007ky2

Botulism Neurooxin Light Chain A app form

• PDB DOI: https://doi.org/10.2210/pdb7KY2/pdb

• Classification: TOXIN
• Organism(s): Clostridium botulinum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-12-07 Released: 2021-04-14 
• Deposition Author(s): Ortega, M.E., Salazameda, N.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 
  0.170 (Depositor), 0.143 (DCC) 
• R-Value Work: 
  0.128 (Depositor), 0.124 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Discovery of Dipeptides as Potent Botulinum Neurotoxin A Light-Chain Inhibitors.

Amezcua, M., Cruz, R.S., Ku, A., Moran, W., Ortega, M.E., Salzameda, N.T.

(2021) ACS Med Chem Lett 12: 295-301

• PubMed: 33603978 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00674
• Primary Citation Related Structures: 
  7KY2, 7KYF, 7KYH


• PubMed Abstract: 
  

  The botulinum neurotoxin, the caustic agent that causes botulism, is the most lethal toxin known to man. The neurotoxin composed of a heavy chain (HC) and a light chain (LC) enters neurons and cleaves SNARE proteins, leading to flaccid paralysis, which, in severe occurrences, can result in death. A therapeutic target for botulinum neurotoxin (BoNT) intoxication is the LC, a zinc metalloprotease that directly cleaves SNARE proteins. Herein we report dipeptides containing an aromatic connected to the N-terminus via a sulfonamide and a hydroxamic acid at the C-terminus as BoNT/A LC inhibitors. On the basis of a structure-activity relationship study, 33 was discovered to inhibit the BoNT/A LC with an IC ₅₀ of 21 nM. X-ray crystallography analysis of 30 and 33 revealed that the dipeptides inhibit through a competitive mechanism and identified several key intermolecular interactions.

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Organizational Affiliation: 
• Department of Chemistry & Biochemistry, California State University, Fullerton, California 92831, United States.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.13 kDa 
• Atom Count: 6,419 
• Modeled Residue Count: 786 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bont/A1	A, B	426	Clostridium botulinum	Mutation(s): 0
UniProt
Find proteins for P0DPI1 (Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)) Explore P0DPI1  Go to UniProtKB:  P0DPI1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free:  0.170 (Depositor), 0.143 (DCC) 
• R-Value Work:  0.128 (Depositor), 0.124 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.029	α = 90
b = 56.985	β = 90.26
c = 192.136	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XPREP	data scaling
PDB_EXTRACT	data extraction
Aimless	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-14 
Deposition Author(s): Ortega, M.E., Salazameda, N.T.

Revision History  

• Version 1.0: 2021-04-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description