3UFA

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


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:  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 function ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease splA
A, B
200Staphylococcus aureus (strain NCTC 8325)Gene Names: splA
EC: 3.4.21.-
Find proteins for Q2FXC2 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FXC2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
VPF
Query on VPF

Download SDF File 
Download CCD File 
A, B
N-(3-carboxypropanoyl)-L-valyl-N-[(1S)-2-phenyl-1-phosphonoethyl]-L-prolinamide
C22 H32 N3 O8 P
KPGFVOVOBVGIMY-QRFRQXIXSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000908 (VPF)
Query on PRD_000908
A,BN-(3-CARBOXYPROPANOYL)-L-VALYL-N-[(1S)-2-PHENYL-1-PHOSPHONOETHYL]-L-PROLINAMIDEPeptide-like / Inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VPFKi: 10000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 61.232α = 90.00
b = 61.232β = 90.00
c = 221.123γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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