3WYI | pdb_00003wyi

Structure of S. aureus undecaprenyl diphosphate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.227 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.188 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3WYI

This is version 1.3 of the entry. See complete history

Literature

Antibacterial drug leads: DNA and enzyme multitargeting.

Zhu, W.Wang, Y.Li, K.Gao, J.Huang, C.H.Chen, C.C.Ko, T.P.Zhang, Y.Guo, R.T.Oldfield, E.

(2015) J Med Chem 58: 1215-1227

  • DOI: https://doi.org/10.1021/jm501449u
  • Primary Citation Related Structures: 
    3WYI, 3WYJ, 4U82, 4U8A, 4U8B, 4U8C

  • PubMed Abstract: 

    We report the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG)2 and using DSC were found to increase the melting transition by up to 24 °C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC50 values of 100-500 nM, and we found good correlations (R(2) = 0.89, S. aureus; R(2) = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA ΔTm and UPPS IC50 experimental results together with one computed descriptor. We also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.


  • Organizational Affiliation
    • Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States.

Macromolecule Content 

  • Total Structure Weight: 29.95 kDa 
  • Atom Count: 2,270 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 256 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoprenyl transferase256Staphylococcus aureusMutation(s): 0 
Gene Names: CH52_12785
EC: 2.5.1

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.227 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.188 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.08α = 90
b = 62.08β = 90
c = 133.486γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description