4XM6

Anthrax toxin lethal factor with ligand-induced binding pocket

• PDB DOI: https://doi.org/10.2210/pdb4XM6/pdb

• Classification: TOXIN,HYDROLASE
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-01-14 Released: 2015-11-11 
• Deposition Author(s): Maize, K.M., De la Mora-Rey, T., Finzel, B.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Minnesota Dept. of Employment and Economic Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor.

Maize, K.M., Kurbanov, E.K., Johnson, R.L., Amin, E.A., Finzel, B.C.

(2015) FEBS Lett 589: 3836-3841

• PubMed: 26578066 
• DOI: https://doi.org/10.1016/j.febslet.2015.11.005
• Primary Citation of Related Structures:  
  4XM6, 4XM7, 4XM8


• PubMed Abstract: 
  

  The Bacillus anthracis lethal factor (LF) is one component of a tripartite exotoxin partly responsible for persistent anthrax cytotoxicity after initial bacterial infection. Inhibitors of the zinc metalloproteinase have been investigated as potential therapeutic agents, but LF is a challenging target because inhibitors lack sufficient selectivity or possess poor pharmaceutical properties. These structural studies reveal an alternate conformation of the enzyme, induced upon binding of specific inhibitors, that opens a previously unobserved deep pocket termed S1'(∗) which might afford new opportunities to design selective inhibitors that target this subsite.

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Organizational Affiliation: 

Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 60.99 kDa 
• Atom Count: 4,149 
• Modelled Residue Count: 486 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal factor	A	519	Bacillus anthracis	Mutation(s): 1  Gene Names: lef, pXO1-107, BXA0172, GBAA_pXO1_0172 EC: 3.4.24.83
UniProt
Find proteins for P15917 (Bacillus anthracis) Explore P15917  Go to UniProtKB:  P15917

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
41R	B [auth A]	N~2~-[(4-fluoro-3-methylphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide C16 H25 F N2 O4 S XENBIBQWLKQPNV-OAHLLOKOSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
41R	Binding MOAD:  4XM6	IC50: 9.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.246 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.936	α = 90
b = 76.922	β = 90
c = 138.576	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Maize, K.M., De la Mora-Rey, T., Finzel, B.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI091790-01
Minnesota Dept. of Employment and Economic Development	United States	SPAP-06-0014-P-FY07

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2015-12-02
  Changes: Database references
• Version 1.2: 2015-12-30
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-12-11
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description