5XZ1 | pdb_00005xz1

Crystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418

• PDB DOI: https://doi.org/10.2210/pdb5XZ1/pdb
• NAKB: 5XZ1

• Classification: RNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-07-11 Released: 2018-07-18 
• Deposition Author(s): Kanazawa, H., Tsurumi, N., Kondo, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.190 (DCC) 

Literature

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

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

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.18 kDa 
• Atom Count: 2,025 
• Modeled Residue Count: 88 
• Deposited Residue Count: 88 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*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, C, D	22	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GET	E [auth A], F [auth B], G [auth C], H [auth C]	GENETICIN C20 H40 N4 O10 BRZYSWJRSDMWLG-DJWUNRQOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.01 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.399	α = 90
b = 32.528	β = 95.58
c = 96.484	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Kanazawa, H., Tsurumi, N., Kondo, J.

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references