1QXY

Crystal structure of S. aureus methionine aminopeptidase in complex with a ketoheterocycle 618


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jm034188j
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
methionyl aminopeptidase
A
252Staphylococcus aureusMutation(s): 0 
EC: 3.4.11.18
Find proteins for P0A078 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P0A078
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M2C
Query on M2C

Download CCD File 
A
(2S)-2-AMINO-4-(METHYLSULFANYL)-1-PYRIDIN-2-YLBUTANE-1,1-DIOL
C10 H16 N2 O2 S
JPZQHIBHGCCNKS-QMMMGPOBSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CO
Query on CO

Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M2CIC50:  16000   nM  Binding MOAD
M2CIC50 :  16000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.144 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.97α = 90
b = 76.69β = 104.5
c = 41.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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