3UFA

Crystal structure of the staphylococcal serine protease SplA in complex with a specific phosphonate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Development and binding characteristics of phosphonate inhibitors of SplA protease from Staphylococcus aureus.

Burchacka, E.Zdzalik, M.Niemczyk, J.S.Pustelny, K.Popowicz, G.Wladyka, B.Dubin, A.Potempa, J.Sienczyk, M.Dubin, G.Oleksyszyn, J.

(2014) Protein Sci 23: 179-189

  • DOI: 10.1002/pro.2403
  • Primary Citation of Related Structures:  
    3UFA, 4MVN

  • PubMed Abstract: 
  • Staphylococcus aureus is responsible for a variety of human infections, including life-threatening, systemic conditions. Secreted proteome, including a range of proteases, constitutes the major virulence factor of the bacterium. However, the functions of individual enzymes, in particular SplA protease, remain poorly characterized ...

    Staphylococcus aureus is responsible for a variety of human infections, including life-threatening, systemic conditions. Secreted proteome, including a range of proteases, constitutes the major virulence factor of the bacterium. However, the functions of individual enzymes, in particular SplA protease, remain poorly characterized. Here, we report development of specific inhibitors of SplA protease. The design, synthesis, and activity of a series of α-aminoalkylphosphonate diaryl esters and their peptidyl derivatives are described. Potent inhibitors of SplA are reported, which may facilitate future investigation of physiological function of the protease. The binding modes of the high-affinity compounds Cbz-Phe(P) -(OC6 H4 -4-SO2 CH3 )2 and Suc-Val-Pro-Phe(P) -(OC6 H5 )2 are revealed by high-resolution crystal structures of complexes with the protease. Surprisingly, the binding mode of both compounds deviates from previously characterized canonical interaction of α-aminoalkylphosphonate peptidyl derivatives and family S1 serine proteases.


    Organizational Affiliation

    Division of Medicinal Chemistry and Microbiology, Faculty of Chemistry, Wroclaw University of Technology, Wroclaw, Poland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine protease splAA, B200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: splASAOUHSC_01942
EC: 3.4.21
UniProt
Find proteins for Q2FXC2 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FXC2 
Go to UniProtKB:  Q2FXC2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VPF (Subject of Investigation/LOI)
Query on VPF

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]N-(3-carboxypropanoyl)-L-valyl-N-[(1S)-2-phenyl-1-phosphonoethyl]-L-prolinamide
C22 H32 N3 O8 P
KPGFVOVOBVGIMY-QRFRQXIXSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A], F [auth B], G [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
VPF PDBBind:  3UFA Ki: 1.00e+4 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.232α = 90
b = 61.232β = 90
c = 221.123γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2014-01-22
    Changes: Database references
  • Version 1.2: 2014-03-05
    Changes: Database references