1YRJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 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 proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Bacterial 16 S Ribosomal RNA A Site OligonucleotideA,B23N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AM2
Query on AM2

Download SDF File 
Download CCD File 
A, B
APRAMYCIN
NEBRAMYCIN II, 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AM2IC50: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.250α = 90.00
b = 30.900β = 90.00
c = 45.810γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2016-11-30
    Type: Other