9KSA | pdb_00009ksa

Serine Beta-Lactamase OXA-48 in Complex with MBL/SBL Inhibitor CB1

• PDB DOI: https://doi.org/10.2210/pdb9KSA/pdb

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


• Deposited: 2024-11-29 Released: 2025-09-03 
• Deposition Author(s): Li, G.-B., Wei, S.-Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.261 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

OXA-48 carbapenemase in complex with 7-((1H-pyrazol-1-yl)methyl)-2-hydroxy-2,3-dihydrobenzo[e][1,4,2]dioxaborinine-8-carboxylic acid

Li, G.-B., Wei, S.-Q.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 113.49 kDa 
• Atom Count: 8,374 
• Modeled Residue Count: 966 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	242	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, PHDFNENF_00011 EC: 3.5.2.6
UniProt
Find proteins for Q6XEC0 (Klebsiella pneumoniae) Explore Q6XEC0  Go to UniProtKB:  Q6XEC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EG0 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	2-oxidanyl-7-(pyrazol-1-ylmethyl)-3~{H}-1,4,2-benzodioxaborinine-8-carboxylic acid C12 H11 B N2 O5 VHKIDNUOLGPNSF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B, C, D	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.261 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.596	α = 90
b = 58.701	β = 104.79
c = 105.855	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPX	data processing
autoPX	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Li, G.-B., Wei, S.-Q.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291; 81502989

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release