8EHH

Crystal structure of the class A extended-spectrum beta-lactamase CTX-M-96 in complex with relebactam at 1.03 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb8EHH/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-14 Released: 2023-09-20 
• Deposition Author(s): Power, P., Ghiglione, B., Bonomo, R.A., Rodriguez, M.M., Gutkind, G., Klinke, S.
• Funding Organization(s): National Scientific and Technical Research Council (CONICET), Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.155 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 

Literature

Biochemical and structural evidences of the activity of relebactam as inhibitor of the extended-spectrum beta-lactamase CTX-M-96.

Ghiglione, B., Rodriguez, M.M., Gutkind, G., Bonomo, R.A., Klinke, S., Power, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 28.48 kDa 
• Atom Count: 2,271 
• Modelled Residue Count: 259 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	263	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaCTX-M-12 variant, blaCTX-M EC: 3.5.2.6
UniProt
Find proteins for Q6ZXB6 (Klebsiella pneumoniae) Explore Q6ZXB6  Go to UniProtKB:  Q6ZXB6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MK7 (Subject of Investigation/LOI)	B [auth A]	(2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide C12 H22 N4 O6 S VGHMECNLFQGIJM-MNOVXSKESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 0.155 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.48	α = 90
b = 45.59	β = 90
c = 117.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Power, P., Ghiglione, B., Bonomo, R.A., Rodriguez, M.M., Gutkind, G., Klinke, S.

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Funding Organization	Location	Grant Number
National Scientific and Technical Research Council (CONICET)	Argentina	11220200100191CO
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2018-01550

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 2.0: 2024-03-13
  Type: Coordinate replacement
  Reason: Missing anisotropic B-factor
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary