4XM7 | pdb_00004xm7

Anthrax toxin lethal factor with ligand-induced binding pocket

• PDB DOI: https://doi.org/10.2210/pdb4XM7/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., Finzel, B.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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 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.
Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, 8-101 Weaver-Densford Hall, Minneapolis, MN 55455, United States. Electronic address: [e-mail].

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: 60.94 kDa 
• Atom Count: 4,174 
• Modeled Residue Count: 510 
• 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
41S	B [auth A]	N~2~-[(4-fluoro-3-methoxyphenyl)sulfonyl]-N-hydroxy-N~2~-(2-methylpropyl)-D-valinamide C16 H25 F N2 O5 S GINWIYLMIMGVMO-OAHLLOKOSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.028	α = 90
b = 78.423	β = 90
c = 139.269	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
PHASER	phasing
SCALA	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): Maize, K.M., 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

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