4WET

Crystal structure of E.Coli DsbA in complex with compound 16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Application of Fragment-Based Screening to the Design of Inhibitors of Escherichia coli DsbA.

Adams, L.A.Sharma, P.Mohanty, B.Ilyichova, O.V.Mulcair, M.D.Williams, M.L.Gleeson, E.C.Totsika, M.Doak, B.C.Caria, S.Rimmer, K.Horne, J.Shouldice, S.R.Vazirani, M.Headey, S.J.Plumb, B.R.Martin, J.L.Heras, B.Simpson, J.S.Scanlon, M.J.

(2015) Angew.Chem.Int.Ed.Engl. 54: 2179-2184

  • DOI: 10.1002/anie.201410341
  • Primary Citation of Related Structures:  
  • Also Cited By: 6BR4, 6BQX

  • PubMed Abstract: 
  • The thiol-disulfide oxidoreductase enzyme DsbA catalyzes the formation of disulfide bonds in the periplasm of Gram-negative bacteria. DsbA substrates include proteins involved in bacterial virulence. In the absence of DsbA, many of these proteins do ...

    The thiol-disulfide oxidoreductase enzyme DsbA catalyzes the formation of disulfide bonds in the periplasm of Gram-negative bacteria. DsbA substrates include proteins involved in bacterial virulence. In the absence of DsbA, many of these proteins do not fold correctly, which renders the bacteria avirulent. Thus DsbA is a critical mediator of virulence and inhibitors may act as antivirulence agents. Biophysical screening has been employed to identify fragments that bind to DsbA from Escherichia coli. Elaboration of one of these fragments produced compounds that inhibit DsbA activity in vitro. In cell-based assays, the compounds inhibit bacterial motility, but have no effect on growth in liquid culture, which is consistent with selective inhibition of DsbA. Crystal structures of inhibitors bound to DsbA indicate that they bind adjacent to the active site. Together, the data suggest that DsbA may be amenable to the development of novel antibacterial compounds that act by inhibiting bacterial virulence.


    Organizational Affiliation

    Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052 (Australia) http://www.pharm.monash.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thiol:disulfide interchange protein
A, B
189Escherichia coli (strain B / BL21-DE3)Mutation(s): 0 
Find proteins for A0A0H2UL03 (Escherichia coli (strain B / BL21-DE3))
Go to UniProtKB:  A0A0H2UL03
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WEF
Query on WEF

Download SDF File 
Download CCD File 
A
N-({4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-5-yl}carbonyl)-L-tyrosine
C21 H17 F3 N2 O4 S
VRYKCDADDIVMLC-INIZCTEOSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WEFKd: 444000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.477α = 90.00
b = 47.118β = 96.20
c = 62.588γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata processing
Blu-Icedata collection
Cootmodel building
PHENIXrefinement
SCALAdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)Australia1009785

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-02-18
    Type: Database references
  • Version 1.2: 2017-10-18
    Type: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy