2O45

Structure of the 23S rRNA of the large ribosomal subunit from Deinococcus Radiodurans in complex with the macrolide RU-69874

• PDB DOI: https://doi.org/10.2210/pdb2O45/pdb
• NAKB: 2O45

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


• Deposited: 2006-12-03 Released: 2007-12-04 
• Deposition Author(s): Baram, D., Pyetan, E., Auerbach-Nevo, T., Yonath, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.364 

Literature

Chemical Parameters Influencing Fine Tuning in the Binding of Macrolide Antibiotics to the Ribosomal Tunnel

Baram, D., Pyetan, E., Auerbach-Nevo, T., Yonath, A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 934.38 kDa 
• Atom Count: 59,428 
• Modelled Residue Count: 2,766 
• Deposited Residue Count: 2,880 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
23S rRNA	A	2,880	Deinococcus radiodurans

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RU6	B [auth A]	(3AS,4R,7R,8S,9S,10R,11R,13R,15R,15AR)-4-ETHYL-11-METHOXY-3A,7,9,11,13,15-HEXAMETHYL-2,6,14-TRIOXO-1-[4-(4-PYRIDIN-3-YL-1H-IMIDAZOL-1-YL)BUTYL]-10-{[3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}TETRADECAHYDRO-2H-OXACYCLOTETRADECINO[4,3-D][1,3]OXAZOL-8-YL 2,6-DIDEOXY-3-C-METHYL-3-O-METHYL-ALPHA-L-RIBO-HEXOPYRANOSIDE C51 H81 N5 O13 LSUFMKOMGWIEMZ-IBNZHXLDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.364 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.01	α = 90
b = 411.475	β = 90
c = 697.616	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Baram, D., Pyetan, E., Auerbach-Nevo, T., Yonath, A.

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description