1YRJ

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

Structural Biology Knowledgebase: 1YRJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.307
  • R-Value Work: 0.246

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YRJ

Classification: RNA

Total Structure Weight: 15853.49

Macromolecule Entities
Molecule Chains Length Organism Details
Bacterial 16 S Ribosomal RNA A Site Oligonucleotide A, B 23 synthetic

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AM2
Query on AM2

A, B APRAMYCIN
3, (Synonym)
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AM2 N/A in BindingDB
N/A in BindingMoad
IC50: 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 = 92.25 α = 90.00
b = 30.90 β = 90.00
c = 45.81 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2005-02-03
  • 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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4