2YDU | pdb_00002ydu

Crystal structure of YopH in complex with 3-(1,1-dioxido-3- oxoisothiazolidin-5-yl)benzaldeyde

• PDB DOI: https://doi.org/10.2210/pdb2YDU/pdb

• Classification: HYDROLASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-24 Released: 2011-11-02 
• Deposition Author(s): Lountos, G.T., Kim, S.E., Bahta, M., Ulrich, R.G., Waugh, D.S., Burke, T.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Isothiazolidinone (Izd) as a Phosphoryl Mimetic in Inhibitors of the Yersinia Pestis Protein Tyrosine Phosphatase Yoph.

Kim, S.E., Bahta, M., Lountos, G.T., Ulrich, R.G., Burke, T.R., Waugh, D.S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 639

• PubMed: 21697602 
• DOI: https://doi.org/10.1107/S0907444911018610
• Primary Citation Related Structures: 
  2YDU


• PubMed Abstract: 
  

  Isothiazolidinone (IZD) heterocycles can act as effective components of protein tyrosine phosphatase (PTP) inhibitors by simultaneously replicating the binding interactions of both a phosphoryl group and a highly conserved water molecule, as exemplified by the structures of several PTP1B-inhibitor complexes. In the first unambiguous demonstration of IZD interactions with a PTP other than PTP1B, it is shown by X-ray crystallography that the IZD motif binds within the catalytic site of the Yersinia pestis PTP YopH by similarly displacing a highly conserved water molecule. It is also shown that IZD-based bidentate ligands can inhibit YopH in a nonpromiscuous fashion at low micromolar concentrations. Hence, the IZD moiety may represent a useful starting point for the development of YopH inhibitors.

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Organizational Affiliation: 
• Chemical Biology Laboratory, National Cancer Institute at Frederick, MD 21702-1201, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 33.79 kDa 
• Atom Count: 2,479 
• Modeled Residue Count: 282 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OUTER PROTEIN H PHOSPHATASE	A	306	Yersinia pestis	Mutation(s): 0  EC: 3.1.3.48
UniProt
Find proteins for O68720 (Yersinia pestis) Explore O68720  Go to UniProtKB:  O68720

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
79W	B [auth A]	3-[(2S)-1,1-DIOXIDO-4-OXOTETRAHYDROTHIOPHEN-2-YL]BENZALDEHYDE C11 H10 O4 S YIJQNPNARRVHGF-NSHDSACASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.307	α = 90
b = 55.912	β = 90
c = 99.055	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Lountos, G.T., Kim, S.E., Bahta, M., Ulrich, R.G., Waugh, D.S., Burke, T.R.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description