2G5K

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


Experimental Data Snapshot

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

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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


Macromolecules
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Entity ID: 1
MoleculeChainsLengthOrganismImage
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 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],
F [auth B]
APRAMYCIN
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
 Ligand Interaction
NCO
Query on NCO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
COBALT HEXAMMINE(III)
Co H18 N6
DYLMFCCYOUSRTK-FGTKAUEHAT
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding 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 = 33.123α = 90
b = 33.123β = 90
c = 116.421γ = 120
Software Package:
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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