9W7P image
Deposition Date 2025-08-06
Release Date 2025-11-19
Last Version Date 2025-11-19
Entry Detail
PDB ID:
9W7P
Keywords:
HYDROLASE
Title:
Crystal Structure of Ledaborbactam in complex with SME-1 class A Carbapenemase
Biological Source:
Source Organism:
Serratia marcescens (Taxon ID: 615)
Host Organism:
Escherichia coli BL21(DE3)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.20 Å
R-Value Free:
0.25
R-Value Work:
0.19
Space Group:
P 1 21 1
9W7P validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Beta-lactamase SME-1
Gene (Uniprot):smeA
Chain IDs:A (auth: B), B (auth: A)
Chain Length:267
Number of Molecules:2
Biological Source:Serratia marcescens
UniProt ID:P52682 Pfam ID:PF00144, PF13354
Ligand Molecules
A1MBD
CL
Primary Citation
Beyond structure and activity: targeting class A carbapenemases with monocyclic and bicyclic boronic acids to counter antimicrobial resistance.
Org.Biomol.Chem. ? ? ? (2025)
PMID: 41217385 DOI: 10.1039/d5ob01703c

Abstact

Bicyclic boronic acids inhibit SME-1 carbapenemase via a unique π-π stacking with His105 and covalent interaction with Ser70. Ledaborbactam shows the strongest inhibition, with the lowest ki and enhanced structural stability. X-ray crystallography and molecular dynamics reveal key features helpful in structure-based optimization of boronates targeting class A β-lactamases.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
9W7P
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