ISDA: 4P20

Deposition Date 2014-02-28

Release Date 2014-05-07

Last Version Date 2023-12-27

Entry Detail

PDB ID:

4P20

Keywords:

RNA/ANTIBIOTIC

Title:

Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

Biological Source:

Source Organism:

synthetic construct (Taxon ID: 32630)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

Space Group:

P 1 21 1

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
Chain IDs:A, B
Chain Length:23
Number of Molecules:2
Biological Source:synthetic construct

Ligand Molecules

AKN

Primary Citation

Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.

Kondo, J, Francois, B, Russell, R.J, Murray, J.B, Westhof, E.Show

Biochimie 88 1027 1031 (2006)

PMID: 16806634 DOI: 10.1016/j.biochi.2006.05.017

Abstact

Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site.

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Primary Citation of related structures

Abstact

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