2HCJ

"Trypsin-modified Elongation Factor Tu in complex with tetracycline"


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular complementarity between tetracycline and the GTPase active site of elongation factor Tu.

Heffron, S.E.Mui, S.Aorora, A.Abel, K.Bergmann, E.Jurnak, F.

(2006) Acta Crystallogr.,Sect.D 62: 1392-1400

  • DOI: 10.1107/S0907444906035426
  • Primary Citation of Related Structures:  2HDN

  • PubMed Abstract: 
  • Two crystal forms of a complex between trypsin-modified elongation factor Tu-MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1 A, respectively. In the P2(1) form, ...

    Two crystal forms of a complex between trypsin-modified elongation factor Tu-MgGDP from Escherichia coli and the antibiotic tetracycline have been solved by X-ray diffraction analysis to resolutions of 2.8 and 2.1 A, respectively. In the P2(1) form, cocrystals were grown from a solution mixture of the protein and tetracycline. Six copies of the trypsin-modified EF-Tu-MgGDP-tetracycline complex are arranged as three sets of dimers in the asymmetric unit. In the second crystal form, tetracycline was diffused into P4(3)2(1)2 crystals, resulting in a monomeric complex in the asymmetric unit. Atomic coordinates have been refined to crystallographic R factors of 18.0% for the P2(1) form and 20.0% for the P4(3)2(1)2 form. In both complexes, tetracycline makes significant interactions with the GTPase active site of EF-Tu. The phenoldiketone moiety of tetracycline interacts directly with the Mg(2+), the alpha-phosphate group of GDP and two amino acids, Thr25 and Asp80, which are conserved in the GX(4)GKS/T and DX(2)G sequence motifs found in all GTPases and many ATPases. The molecular complementarity, previously unrecognized between invariant groups present in all GTPase/ATPases and the active moiety of tetracycline, may have wide-ranging implications for all drugs containing the phenoldiketone moiety as well as for the design of new compounds targeted against a broad range of GTPases or ATPases.


    Organizational Affiliation

    Department of Physiology and Biophysics, 346-D Med Sci I, University of California, Irvine, CA 92697-4560, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein chain elongation factor EF-Tu
A
37Escherichia coli (strain K12)Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein chain elongation factor EF-Tu
B
335Escherichia coli (strain K12)Gene Names: tufA
Find proteins for P0CE47 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE47
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
TAC
Query on TAC

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B
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
 Ligand Interaction
NA
Query on NA

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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GLV
Query on GLV

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B
GLYOXYLIC ACID
GLYOXALATE, GLYOXYLATE
C2 H2 O3
HHLFWLYXYJOTON-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.200 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.110α = 90.00
b = 69.110β = 90.00
c = 157.330γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance