4LC0

Identifying ligand binding hot spots in proteins using brominated fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.221 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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.

(2013) Acta Crystallogr.,Sect.F 69: 1060-1065

  • DOI: 10.1107/S1744309113018551
  • Primary Citation of Related Structures:  

  • 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 ...

    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.


    Organizational Affiliation

    Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England. m.k.groftehauge@dur.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu-A
A
404Thermus thermophilusMutation(s): 0 
Gene Names: tufA (tuf)
Find proteins for P60338 (Thermus thermophilus)
Go to UniProtKB:  P60338
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NH4
Query on NH4

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Download CCD File 
A
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.221 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.830α = 90.00
b = 98.440β = 95.79
c = 39.700γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-11
    Type: Initial release