1YRJ

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
Bacterial 16 S Ribosomal RNA A Site OligonucleotideA, B 23N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AM2
Query on AM2

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
APRAMYCIN
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
F [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 92.25α = 90
b = 30.9β = 90
c = 45.81γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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