Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.16 kDa 
• Atom Count: 1055 
• Modelled Residue Count: 44 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

2G5K

Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin

• PDB DOI: 10.2210/pdb2G5K/pdb
• NDB: DR0030

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-02-23 Released: 2006-06-20 
• Deposition Author(s): Kondo, J., Francois, B., Urzhumtsev, A., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.258 

Literature

Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin

Kondo, J., Francois, B., Urzhumtsev, A., Westhof, E.

(2006) Angew Chem Int Ed Engl 45: 3310-3314

• PubMed: 16596680 
• DOI: 10.1002/anie.200600354
• Primary Citation of Related Structures:  
  2G5K

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'	A, B	23	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AM2	C [auth A], F [auth B]	APRAMYCIN C21 H41 N5 O11 XZNUGFQTQHRASN-XQENGBIVSA-N
NCO	E [auth A], H [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-FGTKAUEHAT
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AM2	PDBBind:  2G5K	Kd: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.258 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.123	α = 90
b = 33.123	β = 90
c = 116.421	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-23 
• Released Date: 2006-06-20 
Deposition Author(s): Kondo, J., Francois, B., Urzhumtsev, A., Westhof, E.

Revision History  

• Version 1.0: 2006-06-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance