1QF5

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

• PDB DOI: https://doi.org/10.2210/pdb1QF5/pdb

• Classification: LIGASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1999-04-06 Released: 1999-12-02 
• Deposition Author(s): Hanessian, S., Lu, P.-P., Sanceau, J.-Y., Chemla, P., Prade, L., Gohda, K., Cowan-Jacob, S.W., Fonne-Pfister, R.

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Experimental Data Snapshot

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

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

• PubMed: 10556888 
• DOI: https://doi.org/10.1002/(sici)1521-3773(19991102)38:21<3159::aid-anie3159>3.0.co;2-2
• Primary Citation of Related Structures:  
  1QF4, 1QF5


• 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 complexes were determined.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 48.29 kDa 
• Atom Count: 3,507 
• Modelled Residue Count: 431 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ADENYLOSUCCINATE SYNTHETASE)	A	431	Escherichia coli	Mutation(s): 0  EC: 6.3.4.4
UniProt
Find proteins for P0A7D4 (Escherichia coli (strain K12)) Explore P0A7D4  Go to UniProtKB:  P0A7D4

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RPL	E [auth A]	(C8-S)-HYDANTOCIDIN 5'-PHOSPHATE C13 H22 N3 O13 P MAXSFYCTFIBEAR-FUIMDIGMSA-N
GDP	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RPL	PDBBind:  1QF5	IC50: 43 (nM) from 1 assay(s)
	Binding MOAD:  1QF5	IC50: 43 (nM) from 1 assay(s)

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 = 81.75	α = 90
b = 81.75	β = 90
c = 158.7	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-02 
Deposition Author(s): Hanessian, S., Lu, P.-P., Sanceau, J.-Y., Chemla, P., Prade, L., Gohda, K., Cowan-Jacob, S.W., Fonne-Pfister, R.

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
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description