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 
  • R-Value Observed: 0.219 

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This is version 1.3 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: https://doi.org/10.1016/j.bbagen.2013.09.006
  • Primary Citation of Related Structures:  
    2X8M, 2X8P

  • 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, 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLINE-BINDING PROTEIN F311Streptococcus pneumoniae R6Mutation(s): 0 
UniProt
Find proteins for Q8DR52 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DR52 
Go to UniProtKB:  Q8DR52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DR52
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X8M
Query on X8M
Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
H [auth A]		IPRATROPIUM
C20 H30 N O3
OEXHQOGQTVQTAT-KKKDIUQISA-N
CHT
Query on CHT
Download Ideal Coordinates CCD File 
L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
CHOLINE ION
C5 H14 N O
OEYIOHPDSNJKLS-UHFFFAOYSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
G [auth A]
I [auth A]
J [auth A]
C [auth A],
E [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.335α = 90
b = 115.69β = 90
c = 73.201γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Version format compliance
  • Version 1.2: 2013-11-13
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description