1QXW

Crystal structure of Staphyloccocus aureus in complex with an aminoketone inhibitor 54135.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of staphylococcusaureus methionine aminopeptidase complexed with keto heterocycle and aminoketone inhibitors reveal the formation of a tetrahedral intermediate.

Douangamath, A.Dale, G.E.D'Arcy, A.Almstetter, M.Eckl, R.Frutos-Hoener, A.Henkel, B.Illgen, K.Nerdinger, S.Schulz, H.MacSweeney, A.Thormann, M.Treml, A.Pierau, S.Wadman, S.Oefner, C.

(2004) J Med Chem 47: 1325-1328

  • DOI: https://doi.org/10.1021/jm034188j
  • Primary Citation of Related Structures:  
    1QXW, 1QXY, 1QXZ

  • PubMed Abstract: 

    High-resolution crystal structures of Staphylococcus aureus methionine aminopeptidase I in complex with various keto heterocycles and aminoketones were determined, and the intermolecular ligand interactions with the enzyme are reported. The compounds are effective inhibitors of the S. aureus enzyme because of the formation of an uncleavable tetrahedral intermediate upon binding. The electron densities unequivocally show the enzyme-catalyzed transition-state analogue mimicking that for amide bond hydrolysis of substrates.


  • Organizational Affiliation

    Morphochem AG, WRO-1055/388, Schwarzwaldallee 215, CH-4058 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
methionyl aminopeptidase252Staphylococcus aureusMutation(s): 0 
EC: 3.4.11.18
UniProt
Find proteins for P0A078 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P0A078 
Go to UniProtKB:  P0A078
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A078
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.993α = 90
b = 76.843β = 104.19
c = 41.935γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations