4P20

Crystal structures of the bacterial ribosomal decoding site complexed with amikacin

• PDB DOI: https://doi.org/10.2210/pdb4P20/pdb
• Entry: 4P20 supersedes: 2G5Q
• NAKB: 4P20

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


• Deposited: 2014-02-28 Released: 2014-05-07 
• Deposition Author(s): Kondo, J., Francois, B., Russell, R.J.M., Murray, J.B., Westhof, E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.213 

Literature

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.

(2006) Biochimie 88: 1027-1031

• PubMed: 16806634 
• DOI: https://doi.org/10.1016/j.biochi.2006.05.017
• Primary Citation of Related Structures:  
  4P20


• PubMed Abstract: 
  

  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.

---

Organizational Affiliation: 

Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université Louis-Pasteur, 15, rue René-Descartes, 67084 Strasbourg, France.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.88 kDa 
• Atom Count: 1,053 
• Modelled Residue Count: 42 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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'	A, B	23	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AKN	C [auth A], D [auth B]	(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide C22 H43 N5 O13 LKCWBDHBTVXHDL-RMDFUYIESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.268 
• R-Value Work: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.55	α = 90
b = 32.82	β = 108.71
c = 52.66	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-07 
Deposition Author(s): Kondo, J., Francois, B., Russell, R.J.M., Murray, J.B., Westhof, E.
• This entry supersedes: 2G5Q

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2015-01-07
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary