1J7T

Complex between Paromomycin and the 16S-rRNA A-site at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb1J7T/pdb
NAKB: 1J7T

Classification: RNA
Mutation(s): No

Deposited: 2001-05-18 Released: 2002-05-18
Deposition Author(s): Vicens, Q., Westhof, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.247
R-Value Work: 0.206

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site.

Vicens, Q., Westhof, E.

(2001) Structure 9: 647-658

PubMed: 11587639 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(01)00629-3
Primary Citation of Related Structures:
1J7T

PubMed Abstract:
Aminoglycoside antibiotics interfere with translation in both gram-positive and gram-negative bacteria by binding to the tRNA decoding A site of the 16S ribosomal RNA.

Organizational Affiliation

Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisation et simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, Cedex 67084, Strasbourg, France.

Macromolecule Content

Total Structure Weight: 15.33 kDa
Atom Count: 1,036
Modelled Residue Count: 42
Deposited Residue Count: 44
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(CPGPCPGPUPCPAPCPAPCPCPGPGPUPGPAPAPGPUPCPGPC)-3'	A, B	22	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAR Query on PAR 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]	PAROMOMYCIN C₂₃ H₄₅ N₅ O₁₄ UOZODPSAJZTQNH-LSWIJEOBSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.247
R-Value Work: 0.206
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33	α = 90
b = 45.9	β = 90
c = 95.3	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-05-18

Deposition Author(s):

Vicens, Q.

Westhof, E.

Revision History (Full details and data files)

Version 1.0: 2002-05-18
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-04-03
Changes: Refinement description