9L77 | pdb_00009l77

Serine Beta-Lactamase OXA-48 in complex with Dual MBL/SBL inhibitor B33

• PDB DOI: https://doi.org/10.2210/pdb9L77/pdb

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


• Deposited: 2024-12-26 Released: 2025-12-31 
• Deposition Author(s): Li, G.-B., Liang, G.-Q.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

A class of novel, potent,dual-acting benzoquinte-borate Beta-lactamase inhibitors targeting SBL/MBL

Li, G.-B., Liang, G.-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: 113.39 kDa 
• Atom Count: 9,089 
• Modeled Residue Count: 964 
• 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 A0A866WQ05 (Klebsiella pneumoniae) Explore A0A866WQ05  Go to UniProtKB:  A0A866WQ05

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EIQ (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	(3~{R})-3-[(3~{R})-6-fluoranyl-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]-2-methylidene-butanoic acid C12 H12 B F O4 PGNFEWJWFZLGLG-KSBSHMNSSA-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: 1.50 Å
• R-Value Free:  0.171 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.406	α = 90
b = 106.039	β = 107.75
c = 94.024	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Li, G.-B., Liang, G.-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: 2025-12-31
  Type: Initial release