1QXW

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

• PDB DOI: https://doi.org/10.2210/pdb1QXW/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-09 Released: 2004-03-16 
• Deposition Author(s): Douangamath, A., Dale, G.E., D'Arcy, A., Oefner, C.

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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 

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

• PubMed: 14998322 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.97 kDa 
• Atom Count: 2,319 
• Modelled Residue Count: 249 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
methionyl aminopeptidase	A	252	Staphylococcus aureus	Mutation(s): 0  EC: 3.4.11.18
UniProt
Find proteins for P0A078 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P0A078  Go to UniProtKB:  P0A078

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M1C	F [auth A]	(3S)-3-AMINO-1-(CYCLOPROPYLAMINO)HEPTANE-2,2-DIOL C10 H22 N2 O2 AYBDGNNJGBFOBQ-VIFPVBQESA-N
ACT	D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M1C	PDBBind:  1QXW	IC50: 7000 (nM) from 1 assay(s)

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 = 40.993	α = 90
b = 76.843	β = 104.19
c = 41.935	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): Douangamath, A., Dale, G.E., D'Arcy, A., Oefner, C.

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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations