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), 0.202 (DCC)
R-Value Work:
0.193 (Depositor), 0.197 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 5XZ1

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
Modeled Residue Count: 88
Deposited Residue Count: 88
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
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 H [auth C] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	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 (Depositor), 0.202 (DCC)
R-Value Work: 0.193 (Depositor), 0.197 (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

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Ligand Structure Quality Assessment

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.