1QF5

DESIGN, SYNTHESIS, AND X-RAY CRYSTAL STRUCTURE OF AN ENZYME BOUND BISUBSTRATE HYBRID INHIBITOR OF ADENYLOSUCCINATE SYNTHETASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An enzyme-bound bisubstrate hybrid inhibitor of adenylosuccinate synthetase

Hanessian, S.Lu, P.P.Sanceau, J.Y.Chemla, P.Gohda, K.Fonne-Pfister, R.Prade, L.Cowan-Jacob, S.W.

(1999) Angew Chem Int Ed Engl 38: 3159-3162

  • DOI: 10.1002/(sici)1521-3773(19991102)38:21<3159::aid-anie3159>3.0.co;2-2
  • Primary Citation of Related Structures:  
    1QF5, 1QF4

  • PubMed Abstract: 
  • Two relatively weak herbicides, hydantocidin phosphate and hadacidin were linked by a C(3) chain to afford a potent inhibitor (the 2S hybrid is shown) of the enzyme adenylosuccinate synthetase. The crystal structures of the bisubstrate-enzyme complex ...

    Two relatively weak herbicides, hydantocidin phosphate and hadacidin were linked by a C(3) chain to afford a potent inhibitor (the 2S hybrid is shown) of the enzyme adenylosuccinate synthetase. The crystal structures of the bisubstrate-enzyme complexes were determined.


    Related Citations: 
    • Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin.
      Poland, B.W., Lee, S.F., Subramanian, M.V., Siehl, D.L., Anderson, R.J., Fromm, H.J., Honzatko, R.B.
      (1996) Biochemistry 35: 15753
    • Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli.
      Silva, M.M., Poland, B.W., Hoffman, C.R., Fromm, H.J., Honzatko, R.B.
      (1995) J Mol Biol 254: 431
    • Crystal structure of adenylosuccinate synthetase from Escherichia coli. Evidence for convergent evolution of GTP-binding domains.
      Poland, B.W., Silva, M.M., Serra, M.A., Cho, Y., Kim, K.H., Harris, E.M., Honzatko, R.B.
      (1993) J Biol Chem 268: 25334

    Organizational Affiliation

    Department of Chemistry, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montreal, QC, H3C 3J7 (Canada).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (ADENYLOSUCCINATE SYNTHETASE)A431Escherichia coliMutation(s): 0 
EC: 6.3.4.4
Find proteins for P0A7D4 (Escherichia coli (strain K12))
Explore P0A7D4 
Go to UniProtKB:  P0A7D4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RPL
Query on RPL

Download CCD File 
A
(C8-S)-HYDANTOCIDIN 5'-PHOSPHATE
C13 H22 N3 O13 P
MAXSFYCTFIBEAR-FUIMDIGMSA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RPLIC50:  43   nM  Binding MOAD
RPLIC50 :  43   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.75α = 90
b = 81.75β = 90
c = 158.7γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-02
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Database references