4LBY

Identifying ligand binding hot spots in proteins using brominated fragments

Summary for 4LBY

• Entry DOI: 10.2210/pdb4lby/pdb
• Related: 4LBV 4LBW 4LBZ 4LC0
• Descriptor: Elongation factor Tu-A, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: gtpase, protein binding
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm: P60338
• Total number of polymer chains: 1
• Total formula weight: 45751.68

Authors

Groftehauge, M.K.,Therkelsen, M.,Taaning, R.,Skrydstrup, T.,Morth, J.P.,Nissen, P. (deposition date: 2013-06-21, release date: 2013-09-11, Last modification date: 2023-09-20)

Primary citation

Grftehauge, M.K.,Therkelsen, M.O.,Taaning, R.,Skrydstrup, T.,Morth, J.P.,Nissen, P.
Identifying ligand-binding hot spots in proteins using brominated fragments.
Acta Crystallogr.,Sect.F, 69:1060-1065, 2013

PubMed Abstract: High-quality crystals of Thermus thermophilus EF-Tu in the GTP-bound conformation at 1.7-2.7 Å resolution were used to test 18 small organic molecules, all brominated for confident identification in the anomalous difference maps. From this relatively small collection, it was possible to identify a small molecule bound in the functionally important tRNA CCA-end binding pocket. The antibiotic GE2270 A is known to interact with the same pocket in EF-Tu and to disrupt the association with tRNA. Bromide could be located from peaks in the anomalous map in data truncated to very low resolution without refining the structure. Considering the speed with which diffraction data can be collected today, it is proposed that it is worthwhile to collect the extra data from fragment screens while crystals are at hand to increase the knowledge of biological function and drug binding in an experimental structural context.

PubMed: 23989163
DOI: 10.1107/S1744309113018551

Experimental method

X-RAY DIFFRACTION (2.692 Å)