5Z71 | pdb_00005z71

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

PDB DOI: https://doi.org/10.2210/pdb5Z71/pdb
NAKB: 5Z71

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

Deposited: 2018-01-26 Released: 2019-01-30
Deposition Author(s): Kanazawa, H., Tsurumi, N., Kondo, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.305 (Depositor), 0.321 (DCC)
R-Value Work:
0.270 (Depositor), 0.289 (DCC)
R-Value Observed:
0.273 (Depositor)

wwPDB Validation 3D Report Full Report

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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: 14.6 kDa
Atom Count: 910
Modeled Residue Count: 41
Deposited Residue Count: 44
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (5'-R(PUPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGPUPCPGPC)-3')	A, B	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 C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	GENETICIN C₂₀ H₄₀ N₄ O₁₀ BRZYSWJRSDMWLG-DJWUNRQOSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.305 (Depositor), 0.321 (DCC)
R-Value Work: 0.270 (Depositor), 0.289 (DCC)
R-Value Observed: 0.273 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.924	α = 90
b = 90.106	β = 90
c = 46.701	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

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

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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.