Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.90 kDa 
• Atom Count: 1658 
• Modelled Residue Count: 193 
• Deposited Residue Count: 203 
• Unique protein chains: 1

3STR

Strep Peptide Deformylase with a time dependent thiazolidine hydroxamic acid

• PDB DOI: 10.2210/pdb3STR/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Streptococcus pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-11 Released: 2011-07-27 
• Deposition Author(s): Campobasso, N., Ward, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.230 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Understanding the origins of time-dependent inhibition by polypeptide deformylase inhibitors.

Totoritis, R., Duraiswami, C., Taylor, A.N., Kerrigan, J.J., Campobasso, N., Smith, K.J., Ward, P., King, B.W., Murrayz-Thompson, M., Jones, A.D., Van Aller, G.S., Aubart, K.M., Zalacain, M., Thrall, S.H., Meek, T.D., Schwartz, B.

(2011) Biochemistry 50: 6642-6654

• PubMed: 21711014 
• DOI: 10.1021/bi200655g
• Primary Citation of Related Structures:  
  3STR, 3SVJ, 3SW8


• PubMed Abstract: 
  

The continual bacterial adaptation to antibiotics creates an ongoing medical need for the development of novel therapeutics. Polypeptide deformylase (PDF) is a highly conserved bacterial enzyme, which is essential for viability. It has previously been shown that PDF inhibitors represent a promising new area for the development of antimicrobial agents, and that many of the best PDF inhibitors demonstrate slow, time-dependent binding. To improve our understanding of the mechanistic origin of this time-dependent inhibition, we examined in detail the kinetics of PDF catalysis and inhibition by several different PDF inhibitors. Varying pH and solvent isotope led to clear changes in time-dependent inhibition parameters, as did inclusion of NaCl, which binds to the active site metal of PDF. Quantitative analysis of these results demonstrated that the observed time dependence arises from slow binding of the inhibitors to the active site metal. However, we also found several metal binding inhibitors that exhibited rapid, non-time-dependent onset of inhibition. By a combination of structural and chemical modification studies, we show that metal binding is only slow when the rest of the inhibitor makes optimal hydrogen bonds within the subsites of PDF. Both of these interactions between the inhibitor and enzyme were found to be necessary to observe time-dependent inhibition, as elimination of either leads to its loss.

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Organizational Affiliation: 

Department of Biological Reagents, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase 3	A [auth P]	203	Streptococcus pneumoniae	Mutation(s): 0  Gene Names:  defB, def3, def, def1, def_1, def_2, A5N45_09745, AZJ70_00135, ERS019420_01538, ERS020524_00508, ERS070137_01366, ERS409062_00883, ERS409277_01912, GM528_05680, GM530_07120, GM536_05180, GM537_01960, GM541_02615, NCTC12140_00964, SAMEA104035170_01069, SAMEA104035469_01095, SAMEA104154673_00503, SAMEA2147814_00912, SAMEA2203862_00793, SAMEA2204024_01646, SAMEA2341322_00198, SAMEA2521606_01307, SAMEA2521861_01572, SAMEA2696492_01107, SAMEA2696596_01078, SAMEA2796704_00661, SAMEA3309693_02062, SAMEA3381527_00453, SAMEA3381574_00169, SAMEA3430861_00407, SAMEA3714340_00439, SAMEA4388199_00158, SAMEA4388349_01621 EC: 3.5.1.88
UniProt
Find proteins for Q939R9 (Streptococcus pneumoniae) Explore Q939R9  Go to UniProtKB:  Q939R9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3LI	G [auth P]	(4R)-3-(4-[4-(2-chlorophenyl)piperazin-1-yl]-6-{[2-methyl-6-(methylcarbamoyl)phenyl]amino}-1,3,5-triazin-2-yl)-N-[2-(hydroxyamino)-2-oxoethyl]-1,3-thiazolidine-4-carboxamide C28 H33 Cl N10 O4 S VJGKWQWGYXBKEJ-NRFANRHFSA-N
SO4	C [auth P], D [auth P], E [auth P], F [auth P]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth P]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	B [auth P]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3LI	BindingDB:  3STR	Ki: 334 (nM) from 1 assay(s)
	PDBBind:  3STR	Ki: 3.96 (nM) from 1 assay(s)
	Binding MOAD:  3STR	Ki: 334 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.230 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.274	α = 90
b = 50.274	β = 90
c = 91.486	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-11 
• Released Date: 2011-07-27 
Deposition Author(s): Campobasso, N., Ward, P.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2011-08-17
  Changes: Database references
• Version 1.2: 2014-04-16
  Changes: Other