4F8V

Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)

• PDB DOI: https://doi.org/10.2210/pdb4F8V/pdb
• NAKB: 4F8V

• Classification: RNA/ANTIBIOTIC
• Mutation(s): No 


• Deposited: 2012-05-18 Released: 2012-08-15 
• Deposition Author(s): Kondo, J., Koganei, M., Kasahara, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 

Literature

Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.

Kondo, J., Koganei, M., Kasahara, T.

(2012) ACS Med Chem Lett 3: 741-744

• PubMed: 24900542 
• DOI: https://doi.org/10.1021/ml300145y
• Primary Citation of Related Structures:  
  4F8U, 4F8V


• PubMed Abstract: 
  

  Sisomicin with an unsaturated sugar ring I displays better antibacterial activity than other structurally related aminoglycosides, such as gentamicin, tobramycin, and amikacin. In the present study, we have confirmed by X-ray analyses that the binding mode of sisomicin is basically similar but not identical to that of the related compounds having saturated ring I. A remarkable difference is found in the stacking interaction between ring I and G1491. While the typical saturated ring I with a chair conformation stacks on G1491 through CH/π interactions, the unsaturated ring I of sisomicin with a partially planar conformation can share its π-electron density with G1491 and fits well within the A-site helix.

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Organizational Affiliation: 

Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University , 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.38 kDa 
• Atom Count: 965 
• Modelled Residue Count: 42 
• Deposited Residue Count: 42 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3')	A, B	21	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIS	C [auth A], D [auth B]	(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside C19 H37 N5 O7 URWAJWIAIPFPJE-YFMIWBNJSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.265 
• R-Value Work: 0.226 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.65	α = 90
b = 107.65	β = 90
c = 48.86	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-15 
Deposition Author(s): Kondo, J., Koganei, M., Kasahara, T.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Structure summary
• Version 1.2: 2019-12-25
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations