8U59

EcDsbA soaked with N-(2-fluorophenyl)-5-methylisoxazole-3-carboxamide and N-(4-(thiophen-3-yl)benzyl)cyclohexanamine

• PDB DOI: https://doi.org/10.2210/pdb8U59/pdb

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


• Deposited: 2023-09-12 Released: 2024-09-25 
• Deposition Author(s): Wang, G., Heras, B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

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: 42.87 kDa 
• Atom Count: 3,206 
• Modelled 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
5V9 (Subject of Investigation/LOI)	C [auth A]	~{N}-[(4-thiophen-3-ylphenyl)methyl]cyclohexanamine C17 H21 N S DWSHMNMYXHMEJV-UHFFFAOYSA-N
SW0 (Subject of Investigation/LOI)	D [auth B]	N-(2-fluorophenyl)-5-methyl-1,2-oxazole-3-carboxamide C11 H9 F N2 O2 VZLZHRVTOSUIPW-UHFFFAOYSA-N
CU	E [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.222 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.518	α = 90
b = 64.655	β = 125.83
c = 74.441	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

---

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