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)

Experimental Data Snapshot

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

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A866WQ05
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EIQ (Subject of Investigation/LOI) Query on A1EIQ Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on 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), 0.171 (DCC)
R-Value Work: 0.151 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-31

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-12-31
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.