ISDA: 4LBY

Deposition Date 2013-06-21

Release Date 2013-09-11

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4LBY

Keywords:

PROTEIN BINDING

Title:

Identifying ligand binding hot spots in proteins using brominated fragments

Biological Source:

Source Organism(s):

Thermus thermophilus (Taxon ID: 274)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.69 Å

R-Value Free:

0.20

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

C 1 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongation factor Tu-A
Gene (Uniprot):tufA
Chain IDs:A
Chain Length:404
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P60338 Pfam ID:PF00009, PF03144, PF03143 EC:3.6.5.3

Ligand Molecules

GNP

NH4

SO4

Primary Citation

Identifying ligand-binding hot spots in proteins using brominated fragments.

Grftehauge, M.K, Therkelsen, M.O, Taaning, R, Skrydstrup, T, Morth, J.P, Nissen, P.Show

Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 69 1060 1065 (2013)

PMID: 23989163 DOI: 10.1107/S1744309113018551

Abstact

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.

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Primary Citation of related structures

Abstact

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