9EGR | pdb_00009egr

Crystal structure of oxidised E.coli DsbA in complex with allene

• PDB DOI: https://doi.org/10.2210/pdb9EGR/pdb

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


• Deposited: 2024-11-21 Released: 2024-12-11 
• Deposition Author(s): Balaji, G.R., Tasdan, Y., Ilyichova, O.V., Akhtar, N., Scanlon, M.J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Identification of an Allene Warhead That Selectively Targets a Histidine Residue in the Escherichia coli Oxidoreductase Enzyme DsbA.

Tasdan, Y., Balaji, G.R., Akhtar, N., Ilyichova, O., Cunliffe, T., Heras, B., Strat, L.L., Murray, J., Capuano, B., Scanlon, M.J., Doak, B.C.

(2025) ACS Med Chem Lett 16: 625-630

• PubMed: 40236539 
• DOI: https://doi.org/10.1021/acsmedchemlett.5c00016
• Primary Citation Related Structures: 
  9EGR


• PubMed Abstract: 
  

  Small molecules that covalently modify proteins typically contain an electrophile that selectively reacts with nucleophilic residues in a protein target, such as cysteine, serine, and threonine. Targeting other amino acids is an emerging strategy in covalent probe design. This study reports the discovery and characterization of the covalent reaction between a novel allene warhead and a histidine residue in the active site of the bacterial thiol-disulfide oxidoreductase enzyme Escherichia coli DsbA ( Ec DsbA). Allenes have not been widely reported for their use as covalent warheads. The interaction was characterized by X-ray crystallography, nuclear magnetic resonance spectroscopy, and mass spectrometry. This analysis provided insights into the structure, reaction rate, and selectivity of the allene. Investigation of the reactivity with nucleophilic amino acids revealed that the reaction with the allene warhead shows some specificity for the histidine in the active site of Ec DsbA. Thus, the allene represents a novel histidine-modifying warhead.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Monash University, 381 Royal Parade, Parkville 3052, Australia.
ARC Centre for Fragment-Based Design, Monash University, 381 Royal Parade, Parkville 3052, Australia.
Monash Fragment Platform, Monash University, 381 Royal Parade, Parkville 3052, Australia.
Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, School of Agriculture, Biomedicine and Environment, La Trobe University, Kingsbury Drive, Bundoora 3083, Australia.
Vernalis (R&D) Ltd., Granta Park, Great Abington CB21 6GB, Cambridge, U.K.

Biological Assembly 1  

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

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

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: 46.56 kDa 
• Atom Count: 3,544 
• Modeled Residue Count: 377 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiol:disulfide interchange protein DsbA	A, B	208	Escherichia coli	Mutation(s): 0  Gene Names: dsbA, Z5392, ECs4783
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12)) Explore P0AEG4  Go to UniProtKB:  P0AEG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BH7 (Subject of Investigation/LOI)	C [auth B]	methyl 4-{3-[(5-methyl-1,2-oxazole-3-carbonyl)amino]phenyl}butanoate C16 H18 N2 O4 QXRDFNLRULOJRX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.451	α = 90
b = 65.114	β = 93.861
c = 93.957	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: 2024-12-11 
Deposition Author(s): Balaji, G.R., Tasdan, Y., Ilyichova, O.V., Akhtar, N., Scanlon, M.J.

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

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Database references