5EKW | pdb_00005ekw

A. thaliana IGPD2 in complex with the racemate of the triazole-phosphonate inhibitor, C348

• PDB DOI: https://doi.org/10.2210/pdb5EKW/pdb

• Classification: LYASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-04 Released: 2016-10-05 
• Deposition Author(s): Bisson, C., Britton, K.L., Sedelnikova, S.E., Rodgers, H.F., Eadsforth, T.C., Viner, R.C., Hawkes, T.R., Baker, P.J., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.133 (Depositor), 0.131 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.124 (Depositor) 

Starting Model: experimental

Literature

Mirror-Image Packing Provides a Molecular Basis for the Nanomolar Equipotency of Enantiomers of an Experimental Herbicide.

Bisson, C., Britton, K.L., Sedelnikova, S.E., Rodgers, H.F., Eadsforth, T.C., Viner, R.C., Hawkes, T.R., Baker, P.J., Rice, D.W.

(2016) Angew Chem Int Ed Engl 55: 13485-13489

• PubMed: 27717128 
• DOI: https://doi.org/10.1002/anie.201607185
• Primary Citation Related Structures: 
  5DNL, 5DNX, 5EKW, 5EL9, 5ELW


• PubMed Abstract: 
  

  Programs of drug discovery generally exploit one enantiomer of a chiral compound for lead development following the principle that enantiomer recognition is central to biological specificity. However, chiral promiscuity has been identified for a number of enzyme families, which have shown that mirror-image packing can enable opposite enantiomers to be accommodated in an enzyme's active site. Reported here is a series of crystallographic studies of complexes between an enzyme and a potent experimental herbicide whose chiral center forms an essential part of the inhibitor pharmacophore. Initial studies with a racemate at 1.85 Å resolution failed to identify the chirality of the bound inhibitor, however, by extending the resolution to 1.1 Å and by analyzing high-resolution complexes with the enantiopure compounds, we determined that both enantiomers make equivalent pseudosymmetric interactions in the active site, thus mimicking an achiral reaction intermediate.

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Organizational Affiliation: 
• Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
Division of Biological Chemistry and Drug Discovery, Wellcome Trust Biocentre, University of Dundee, Dundee, DD1 5EH, UK.
Syngenta, Jealott's Hill International Research Station, Bracknell, RG42 6EY, UK.
Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. [e-mail].
Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

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

Macromolecule Content 

• Total Structure Weight: 23.57 kDa 
• Atom Count: 1,882 
• Modeled Residue Count: 194 
• Deposited Residue Count: 205 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase 2, chloroplastic	A	205	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HISN5B, At4g14910, dl3495c EC: 4.2.1.19
UniProt
Find proteins for O23346 (Arabidopsis thaliana) Explore O23346  Go to UniProtKB:  O23346

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5DL	D [auth A]	[(2S)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid C5 H10 N3 O4 P ZXKJPBBOMRHTCH-YFKPBYRVSA-N
5LD	E [auth A]	[(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid C5 H10 N3 O4 P ZXKJPBBOMRHTCH-RXMQYKEDSA-N
TRS	L [auth A], M [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.133 (Depositor), 0.131 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.124 (Depositor) 

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.905	α = 90
b = 112.905	β = 90
c = 112.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Bisson, C., Britton, K.L., Sedelnikova, S.E., Rodgers, H.F., Eadsforth, T.C., Viner, R.C., Hawkes, T.R., Baker, P.J., Rice, D.W.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-10-26
  Changes: Database references
• Version 2.0: 2018-11-28
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-10-09
  Changes: Data collection
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description