3S4P

Crystal structure of the bacterial ribosomal decoding site complexed with an amphiphilic paromomycin O2''-ether analogue

PDB DOI: https://doi.org/10.2210/pdb3S4P/pdb
NAKB: 3S4P

Classification: RNA/ANTIBIOTIC
Mutation(s): No

Deposited: 2011-05-20 Released: 2011-09-21
Deposition Author(s): Szychowski, J., Kondo, J., Zahr, O., Auclair, K., Westhof, E., Hanessian, S., Keillor, J.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.267
R-Value Work: 0.238

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Inhibition of aminoglycoside-deactivating enzymes APH(3')-IIIa and AAC(6')-Ii by amphiphilic paromomycin O2''-ether analogues

Szychowski, J., Kondo, J., Zahr, O., Auclair, K., Westhof, E., Hanessian, S., Keillor, J.W.

(2011) ChemMedChem 6: 1961-1966

PubMed: 21905229 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201100346
Primary Citation of Related Structures:
3S4P

Organizational Affiliation

Department of Chemistry, Université de Montréal, C. P. 6128, Succ. Centre-Ville, Montréal, QC, H3C 3J7, Canada.

Macromolecule Content

Total Structure Weight: 15.01 kDa
Atom Count: 1,044
Modelled Residue Count: 42
Deposited Residue Count: 42
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(PGPCPGPUPCPAPCPAPCPCPGPGPUPGPAPAPGPUPCPGP*C)-3')	A, B	21	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JS6 Query on JS6 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-2-O-{2-[(2-phenylethyl)amino]ethyl}-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside C₃₃ H₅₈ N₆ O₁₄ RYWOYAQAVIFICV-KWRLVFCDSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
JS6	PDBBind: 3S4P	Ki: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free: 0.267
R-Value Work: 0.238
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.189	α = 90
b = 44.689	β = 90
c = 94.585	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2013-06-19
Changes: Database references
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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