8UBQ | pdb_00008ubq

EcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide and 2-benzyl-4-phenylthiazole-5-carboxylic acid

• PDB DOI: https://doi.org/10.2210/pdb8UBQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-09-24 Released: 2024-09-25 
• Deposition Author(s): Wang, G., Heras, B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Two-mode inhibition of DsbA: combination of two site-specific inhibitors enhances virulence inhibition in Salmonella enterica serovar Typhimurium

Wang, G., Heras, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.89 kDa 
• Atom Count: 3,318 
• Modeled Residue Count: 376 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B	189	Escherichia coli K-12	Mutation(s): 0  Gene Names: dsbA, dsf, ppfA, b3860, JW3832
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W9H (Subject of Investigation/LOI)	C [auth A]	2-benzyl-4-phenyl-1,3-thiazole-5-carboxylic acid C17 H13 N O2 S MKDPSENJELZGTK-UHFFFAOYSA-N
SW0	E [auth B]	N-(2-fluorophenyl)-5-methyl-1,2-oxazole-3-carboxamide C11 H9 F N2 O2 VZLZHRVTOSUIPW-UHFFFAOYSA-N
CU	D [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.971	α = 90
b = 64.76	β = 125.93
c = 74.842	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Wang, G., Heras, B.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1099151

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary