Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 934.22 kDa 
• Atom Count: 58817 
• Modelled Residue Count: 2738 
• Deposited Residue Count: 2880 
• Unique nucleic acid chains: 1

1P9X

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

• PDB DOI: 10.2210/pdb1P9X/pdb
• NDB: RR0071

• 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.

---

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 

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: 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.

---

Related Citations: 

• Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Centre in Eubacteria
  Schlunzen, F., Zarivach, R., Harms, J., Bashan, A., Tocilj, A., Albrecht, R., Yonath, A., Franceschi, F.
  (2001) Nature 413: 814

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S RIBOSOMAL RNA	A [auth 0]	2880	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

• Deposited Date: 2003-05-13 
• 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