4PDQ

Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neomycin analog

PDB DOI: https://doi.org/10.2210/pdb4PDQ/pdb
NAKB: 4PDQ

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

Deposited: 2014-04-21 Released: 2015-01-07
Deposition Author(s): Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Feeney, L.A., Armstrong, E.S., Kondo, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis, broad spectrum antibacterial activity, and X-ray co-crystal structure of the decoding bacterial ribosomal A-site with 4'-deoxy-4'-fluoro neomycin analogs

Hanessian, S., Saavedra, O.M., Vilchis-Reyes, M.A., Maianti, J.P., Kanazawa, H., Dozzo, P., Matias, R.D., Serio, A., Kondo, J.

(2014) Chem Sci 5: 4621-4632

DOI: https://doi.org/10.1039/C4SC01626B

Macromolecule Content

Total Structure Weight: 15.51 kDa
Atom Count: 1,026
Modelled Residue Count: 46
Deposited Residue Count: 46
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-UPUPGPCPGPUPCPAPCPGPCPCPGPGPCPGPAPAPGPUPCPGP*C-3')	A, B	23	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMZ Query on NMZ Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	(2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy }-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide C₂₇ H₅₂ F N₇ O₁₄ VWXJAOATJPQONW-MKAHEPKYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B]	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.195
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.657	α = 90
b = 103.657	β = 90
c = 44.572	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
Coot	model building
PHENIX	phasing
PHENIX	model building
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-01-07
Type: Initial release
Version 1.1: 2020-01-22
Changes: Data collection, Derived calculations, Source and taxonomy
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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