5K1D

Crystal structure of a class C beta lactamase/compound1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Literature

GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C beta-Lactamase.

Na, J.H., An, Y.J., Cha, S.S.

(2017) Antimicrob Agents Chemother 61

  • DOI: https://doi.org/10.1128/AAC.00098-17
  • Primary Citation of Related Structures:  
    5K1D, 5K1F

  • PubMed Abstract: 

    Nucleotides were effective in inhibiting the class C β-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a K i value of 16.2 μM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.

    • Organizational Affiliation: 

    Department of Chemistry & Nano Science, Ewha Womans University, Seoul, Republic of Korea.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase366Klebsiella aerogenesMutation(s): 0 
Gene Names: blaCMY-10
EC: 3.5.2.6
UniProt
Find proteins for Q99QC1 (Klebsiella aerogenes)
Explore Q99QC1 
Go to UniProtKB:  Q99QC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99QC1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.625α = 90
b = 59.381β = 90
c = 112.833γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations