2BML | pdb_00002bml

Ofloxacin-like antibiotics inhibit pneumococcal cell wall degrading virulence factors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.280 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Ofloxacin-Like Antibiotics Inhibit Pneumococcal Cell Wall-Degrading Virulence Factors

Fernandez-Tornero, C.Garcia, E.Lopez, R.Pascual-Teresa, B.D.Gimenez-Gallego, G.Romero, A.

(2005) J Biological Chem 280: 19948

  • DOI: https://doi.org/10.1074/jbc.M501236200
  • Primary Citation Related Structures: 
    2BML

  • PubMed Abstract: 

    The search for new drugs against Streptococcus pneumoniae (pneumococcus) is driven by the 1.5 million deaths it causes annually. Choline-binding proteins attach to the pneumococcal cell wall through domains that recognize choline moieties, and their involvement in pneumococcal virulence makes them potential targets for drug development. We have defined chemical criteria involved in the docking of small molecules from a three-dimensional structural library to the major pneumococcal autolysin (LytA) choline binding domain. These criteria were used to identify compounds that could interfere with the attachment of this protein to the cell wall, and several quinolones that fit this framework were found to inhibit the cell wall-degrading activity of LytA. Furthermore, these compounds produced similar effects on other enzymes with different catalytic activities but that contained a similar choline binding domain; that is, autolysin (LytC) and the phage lytic enzyme (Cpl-1). Finally, we resolved the crystal structure of the complex between the choline binding domain of LytA and ofloxacin at a resolution of 2.6 Angstroms. These data constitute an important launch pad from which effective drugs to combat pneumococcal infections can be developed.


  • Organizational Affiliation
    • Departamento de Estructura y Función de Proteínas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.

Macromolecule Content 

  • Total Structure Weight: 31.44 kDa 
  • Atom Count: 2,271 
  • Modeled Residue Count: 251 
  • Deposited Residue Count: 252 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AUTOLYSIN
A, B
126Streptococcus pneumoniaeMutation(s): 0 
EC: 3.5.1.28
UniProt
Find proteins for P06653 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P06653 
Go to UniProtKB:  P06653
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06653
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XED

Query on XED



Download:Ideal Coordinates CCD File
F [auth B]DEXTROFLOXACINE
C18 H20 F N3 O4
GSDSWSVVBLHKDQ-SNVBAGLBSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B]
HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
H [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth B],
J [auth B],
K [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.280 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.67α = 90
b = 94.48β = 90
c = 38.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description