5K1D

Crystal structure of a class C beta lactamase/compound1 complex

• PDB DOI: https://doi.org/10.2210/pdb5K1D/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella aerogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-05-18 Released: 2017-05-17 
• Deposition Author(s): AN, Y.J., Na, J.H., Cha, S.S.

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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 

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

• PubMed: 28242658 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.23 kDa 
• Atom Count: 2,914 
• Modelled Residue Count: 359 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	366	Klebsiella aerogenes	Mutation(s): 0  Gene Names: blaCMY-10 EC: 3.5.2.6
UniProt
Find proteins for Q99QC1 (Klebsiella aerogenes) Explore Q99QC1  Go to UniProtKB:  Q99QC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	B [auth A]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
CD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

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 = 49.625	α = 90
b = 59.381	β = 90
c = 112.833	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): AN, Y.J., Na, J.H., Cha, S.S.

Revision History  

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