5XZ1

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
R-Value Work: 0.193

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.

Macromolecule Content

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

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(UPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGPUPCPGPC)-3')	A, B, C, D	22	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GET Query on GET Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C]	E [auth A], F [auth B], G [auth C], H [auth C]	GENETICIN C₂₀ H₄₀ N₄ O₁₀ BRZYSWJRSDMWLG-DJWUNRQOSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free: 0.199
R-Value Work: 0.193
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-07-18

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.