9RQC

Fragment screening of FosAKP, cryo structure in complex with fragment F2X-entry G02

Summary for 9RQC

• Entry DOI: 10.2210/pdb9rqc/pdb
• Descriptor: FosA family fosfomycin resistance glutathione transferase, methyl [3-(aminomethyl)phenoxy]acetate, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: antibiotic resistance, fosfomycin, fragment screening, transferase
• Biological source: Klebsiella pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 33063.99

Authors

Guenther, S.,Galchenkova, M.,Fischer, P.,Reinke, P.Y.A.,Falke, S.,Thekku Veedu, S.,Rodrigues, A.C.,Senst, J.,Meents, A. (deposition date: 2025-06-25, release date: 2025-10-22)

Primary citation

Gunther, S.,Fischer, P.,Galchenkova, M.,Falke, S.,Reinke, P.Y.A.,Thekku Veedu, S.,Rodrigues, A.C.,Senst, J.,Elinjikkal, D.,Gumprecht, L.,Meyer, J.,Chapman, H.N.,Barthelmess, M.,Meents, A.
Room-temperature X-ray fragment screening with serial crystallography.
Nat Commun, 16:9089-9089, 2025

PubMed Abstract: Structural insights into protein-ligand interactions are essential for advancing drug development, with macromolecular X-ray crystallography being a cornerstone technique. Commonly X-ray data collection is conducted at cryogenic temperatures to mitigate radiation damage effects. However, this can introduce artifacts not only in the protein conformation but also in protein-ligand interactions. Recent studies highlight the advantages of room-temperature (RT) crystallography in capturing relevant states much closer to physiological temperatures. We have advanced fixed-target serial crystallography to enable high-throughput fragment screening at RT. Here we systematically compare RT fragment screening of the Fosfomycin-resistance protein A from Klebsiella pneumoniae (FosAKP), an enzyme involved in antibiotic resistance, with conventional single crystal data collection at cryogenic temperature (cryo). With RT serial crystallography we achieve resolutions comparable to cryogenic methods and identify a previously unobserved conformational state of the active site, offering additional starting points for drug design. For ligands identified in both screens, temperature does not have an influence on the binding mode of the ligand. But overall, we observe more binders at cryo, both at physiologically relevant and non-relevant sites. With the potential for further automation, RT screening with serial crystallography can advance drug development pipelines by making undiscovered conformations of proteins accessible.

PubMed: 41083451
DOI: 10.1038/s41467-025-64918-6

Experimental method

X-RAY DIFFRACTION (1.15 Å)