9EGR | pdb_00009egr

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


Experimental Data Snapshot

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

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This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.5c00016
  • Primary Citation of 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.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Monash University, 381 Royal Parade, Parkville 3052, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiol:disulfide interchange protein DsbA
A, B
208Escherichia coliMutation(s): 0 
Gene Names: dsbAZ5392ECs4783
UniProt
Find proteins for P0AEG4 (Escherichia coli (strain K12))
Explore P0AEG4 
Go to UniProtKB:  P0AEG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEG4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BH7 (Subject of Investigation/LOI)
Query on A1BH7

Download Ideal Coordinates CCD File 
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), 0.219 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.451α = 90
b = 65.114β = 93.861
c = 93.957γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

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