2X8M

Crystal Structure of CbpF in complex with ipratropium by soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Cbpf Complexed with Atropine and Ipratropium Reveal Clues for the Design of Novel Antimicrobials Against Streptococcus Pneumoniae.

Martin, N.S.Retamosa, M.G.Maestro, B.Bartual, S.G.Rodes, M.J.Garcia, P.Sanz, J.M.Hermoso, J.A.

(2013) Biochim.Biophys.Acta 1840: 129

  • DOI: 10.1016/j.bbagen.2013.09.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptococcus pneumoniae is a major pathogen responsible of important diseases worldwide such as pneumonia and meningitis. An increasing resistance level hampers the use of currently available antibiotics to treat pneumococcal diseases. Consequently, ...

    Streptococcus pneumoniae is a major pathogen responsible of important diseases worldwide such as pneumonia and meningitis. An increasing resistance level hampers the use of currently available antibiotics to treat pneumococcal diseases. Consequently, it is desirable to find new targets for the development of novel antimicrobial drugs to treat pneumococcal infections. Surface choline-binding proteins (CBPs) are essential in bacterial physiology and infectivity. In this sense, esters of bicyclic amines (EBAs) such as atropine and ipratropium have been previously described to act as choline analogs and effectively compete with teichoic acids on binding to CBPs, consequently preventing in vitro pneumococcal growth, altering cell morphology and reducing cell viability.


    Organizational Affiliation

    Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física 'Rocasolano', Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CHOLINE-BINDING PROTEIN F
A
311Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: cbpF
Find proteins for Q8DR52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DR52
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
X8M
Query on X8M

Download SDF File 
Download CCD File 
A
IPRATROPIUM
(3-ENDO,8-ANTI)-3-{[(2R)-3-HYDROXY-2-PHENYLPROPANOYL]OXY}-8-METHYL-8-(1-METHYLETHYL)-8-AZONIABICYCLO[3.2.1]OCTANE
C20 H30 N O3
OEXHQOGQTVQTAT-KKKDIUQISA-N
 Ligand Interaction
CHT
Query on CHT

Download SDF File 
Download CCD File 
A
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 52.335α = 90.00
b = 115.690β = 90.00
c = 73.201γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOSFLMdata reduction
MOLREPphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2013-10-02
    Type: Data collection, Database references, Non-polymer description, Refinement description, Version format compliance
  • Version 1.2: 2013-11-13
    Type: Database references