5Z71 | pdb_00005z71

Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.305 (Depositor), 0.320 (DCC) 
  • R-Value Work: 
    0.270 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.273 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structural studies of aminoglycoside antibiotics G418 and its derivatives with readthrough activities

Kanazawa, H., Tsurumi, N., Baasov, T., Kondo, J.

To be published.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(P*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
22synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GET
Query on GET
Download Ideal Coordinates CCD File 
C [auth B]GENETICIN
C20 H40 N4 O10
BRZYSWJRSDMWLG-DJWUNRQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.305 (Depositor), 0.320 (DCC) 
  • R-Value Work:  0.270 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.273 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.924α = 90
b = 90.106β = 90
c = 46.701γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references