Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.91 kDa 
• Atom Count: 6118 
• Residue Count: 716 
• Unique protein chains: 1

1MXO

AmpC beta-lactamase in complex with an m.carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain

• DOI: 10.2210/pdb1MXO/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2002-10-02 Released: 2003-03-04 
• Deposition Author(s): Morandi, F., Caselli, E., Morandi, S., Focia, P.J., Blazquez, J., Shoichet, B.K., Prati, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 

Literature

Nanomolar inhibitors of AmpC beta-lactamase.

Morandi, F., Caselli, E., Morandi, S., Focia, P.J., Blazquez, J., Shoichet, B.K., Prati, F.

(2003) J Am Chem Soc 125: 685-695

• PubMed: 12526668 
• DOI: 10.1021/ja0288338
• Primary Citation of Related Structures:  
  1MXO, 1MY8


• PubMed Abstract: 
  

beta-lactamases are the most widespread resistance mechanism to beta-lactam antibiotics, such as the penicillins and the cephalosporins. In an effort to combat these enzymes, a combination of stereoselective organic synthesis, enzymology, microbiology, and X-ray crystallography was used to design and evaluate new carboxyphenyl-glycylboronic acid transition-state analogue inhibitors of the class C beta-lactamase AmpC. The new compounds improve inhibition by over 2 orders of magnitude compared to analogous glycylboronic acids, with K(i) values as low as 1 nM. On the basis of the differential binding of different analogues, the introduced carboxylate alone contributes about 2.1 kcal/mol in affinity. This carboxylate corresponds to the ubiquitous C3(4)' carboxylate of beta-lactams, and this energy represents the first thermodynamic measurement of the importance of this group in molecular recognition by class C beta-lactamases. The structures of AmpC in complex with two of these inhibitors were determined by X-ray crystallography at 1.72 and 1.83 A resolution. These structures suggest a structural basis for the high affinity of the new compounds and provide templates for further design. The highest affinity inhibitor was 5 orders of magnitude more selective for AmpC than for characteristic serine proteases, such as chymotrypsin. This inhibitor reversed the resistance of clinical pathogens to the third generation cephalosporin ceftazidime; it may serve as a lead compound for drug discovery to combat bacterial resistance to beta-lactam antibiotics.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, University of California, San Francisco, Mission Bay Genentech Hall, 600 16th Street, Mail Box 2240, 94143, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B	358	Escherichia coli	Mutation(s): 0  Gene Names: ampC EC: 3.5.2.6
Find proteins for P00811 (Escherichia coli (strain K12)) Explore P00811  Go to UniProtKB:  P00811

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM2	A, B	(1R)-1-(2-THIENYLACETYLAMINO)-1-(3-CARBOXYPHENYL)METHYLBORONIC ACID C14 H14 B N O5 S HQLQTGGLHBYZSA-ZDUSSCGKSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SM2	Ki :  1   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.957	α = 90
b = 77.488	β = 115.78
c = 96.906	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-10-02 
• Released Date: 2003-03-04 
Deposition Author(s): Morandi, F., Caselli, E., Morandi, S., Focia, P.J., Blazquez, J., Shoichet, B.K., Prati, F.

Revision History 

• Version 1.0: 2003-03-04
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance