1YRJ

Crystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide

• PDB DOI: https://doi.org/10.2210/pdb1YRJ/pdb
• NAKB: 1YRJ

• Classification: RNA
• Mutation(s): No 


• Deposited: 2005-02-03 Released: 2005-06-07 
• Deposition Author(s): Han, Q., Zhao, Q., Fish, S., Simonsen, K.B., Vourloumis, D., Froelich, J.M., Wall, D., Hermann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.307 
• R-Value Work: 0.246 

Starting Model: experimental

Literature

Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.

Han, Q., Zhao, Q., Fish, S., Simonsen, K.B., Vourloumis, D., Froelich, J.M., Wall, D., Hermann, T.

(2005) Angew Chem Int Ed Engl 44: 2694-2700

• PubMed: 15849690 
• DOI: https://doi.org/10.1002/anie.200500028
• Primary Citation of Related Structures:  
  1YRJ

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Organizational Affiliation: 

Department of Structural Chemistry, Anadys Pharmaceuticals, Inc. 3115 Merryfield Row, San Diego, CA 92121, USA, Fax: [phone].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.85 kDa 
• Atom Count: 1,093 
• Modelled Residue Count: 45 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Bacterial 16 S Ribosomal RNA A Site Oligonucleotide	A, B	23	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AM2	C [auth A], E [auth B]	APRAMYCIN C21 H41 N5 O11 XZNUGFQTQHRASN-XQENGBIVSA-N
K	F [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AM2	PDBBind:  1YRJ	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.307 
• R-Value Work: 0.246 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.25	α = 90
b = 30.9	β = 90
c = 45.81	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Han, Q., Zhao, Q., Fish, S., Simonsen, K.B., Vourloumis, D., Froelich, J.M., Wall, D., Hermann, T.

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-11-30
  Changes: Other
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary