1P9X

THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TELITHROMYCIN KETOLIDE ANTIBIOTIC

• PDB DOI: https://doi.org/10.2210/pdb1P9X/pdb
• NAKB: 1P9X

• Classification: RIBOSOME
• Organism(s): Deinococcus radiodurans
• Mutation(s): No 


• Deposited: 2003-05-13 Released: 2003-08-05 
• Deposition Author(s): Berisio, R., Harms, J., Schluenzen, F., Zarivach, R., Hansen, H.A., Fucini, P., Yonath, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.340 
• R-Value Work: 0.273 
• R-Value Observed: 0.280 

Starting Model: experimental

Literature

Structural insight into the antibiotic action of telithromycin against resistant mutants

Berisio, R., Harms, J., Schluenzen, F., Zarivach, R., Hansen, H.A., Fucini, P., Yonath, A.

(2003) J Bacteriol 185: 4276-4279

• PubMed: 12837804 
• DOI: https://doi.org/10.1128/JB.185.14.4276-4279.2003
• Primary Citation of Related Structures:  
  1P9X


• PubMed Abstract: 
  

  The crystal structure of the ketolide telithromycin bound to the Deinococcus radiodurans large ribosomal subunit shows that telithromycin blocks the ribosomal exit tunnel and interacts with domains II and V of the 23S RNA. Comparisons to other clinically relevant macrolides provided structural insights into its enhanced activity against macrolide-resistant strains.

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Organizational Affiliation: 

Max-Planck-Research Unit for Ribosomal Structure, Hamburg, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 934.22 kDa 
• Atom Count: 58,817 
• Modelled Residue Count: 2,738 
• Deposited Residue Count: 2,880 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S RIBOSOMAL RNA	A [auth 0]	2,880	Deinococcus radiodurans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEL	B [auth 0]	TELITHROMYCIN C43 H65 N5 O10 LJVAJPDWBABPEJ-PNUFFHFMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.340 
• R-Value Work: 0.273 
• R-Value Observed: 0.280 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170	α = 90
b = 414.5	β = 90
c = 693	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CCP4	model building
CNS	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-05 
Deposition Author(s): Berisio, R., Harms, J., Schluenzen, F., Zarivach, R., Hansen, H.A., Fucini, P., Yonath, A.

Revision History  

• Version 1.0: 2003-08-05
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-01-27
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description