5UJ3

Crystal structure of the KPC-2 beta-lactamase complexed with hydrolyzed cefotaxime


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2).

Pemberton, O.A.Zhang, X.Chen, Y.

(2017) J. Med. Chem. 60: 3525-3530

  • DOI: 10.1021/acs.jmedchem.7b00158
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbapenem-resistant Enterobacteriaceae are resistant to most β-lactam antibiotics due to the production of the Klebsiella pneumoniae carbapenemase (KPC-2) class A β-lactamase. Here, we present the first product complex crystal structures of KPC-2 wi ...

    Carbapenem-resistant Enterobacteriaceae are resistant to most β-lactam antibiotics due to the production of the Klebsiella pneumoniae carbapenemase (KPC-2) class A β-lactamase. Here, we present the first product complex crystal structures of KPC-2 with β-lactam antibiotics containing hydrolyzed cefotaxime and faropenem. They provide experimental insights into substrate recognition by KPC-2 and its unique cephalosporinase/carbapenemase activity. These structures also represent the first product complexes for a wild-type serine β-lactamase, elucidating the product release mechanism of these enzymes in general.


    Organizational Affiliation

    Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbapenem-hydrolyzing beta-lactamase KPC
A
290Klebsiella pneumoniaeGene Names: bla (kpc, kpc1)
EC: 3.5.2.6
Find proteins for Q9F663 (Klebsiella pneumoniae)
Go to UniProtKB:  Q9F663
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CE4
Query on CE4

Download SDF File 
Download CCD File 
A
(2R)-2-[(R)-{[(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-(methoxyimino)acetyl]amino}(carboxy)methyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
cefotaxime, hydrolyzed, C3'-cleaved, open, unbound form
C14 H15 N5 O6 S2
ZRDXEERHKBZJMY-KTFFUYHOSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.169 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.930α = 90.00
b = 58.780β = 90.00
c = 76.840γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States4R01AI103158-04

Revision History 

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-05-10
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence