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 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

  • Primary Citation of Related Structures:  

  • 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 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (ADENYLOSUCCINATE SYNTHETASE)
A
431Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: purA (adeK)
EC: 6.3.4.4
Find proteins for P0A7D4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7D4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
A
(C8-S)-HYDANTOCIDIN 5'-PHOSPHATE
[8,9-DIHYDROXY-3-(4-CARBOXY-HYDROXY-HYDROXYMETHYL-AMINO-BUTYL)-2,4-DIOXO-6-OXA-1,3-DIAZA-SPIRO[4.4]NON-7-YLMETHYL] PHOSPHATE
C13 H22 N3 O13 P
MAXSFYCTFIBEAR-FUIMDIGMSA-N
 Ligand Interaction
PO4
Query on PO4

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.750α = 90.00
b = 81.750β = 90.00
c = 158.700γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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