2BEE

Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site

Francois, B., Szychowski, J., Adhikari, S.S., Pachamuthu, K., Swayze, E.E., Griffey, R.H., Migawa, M.T., Westhof, E., Hanessian, S.

(2004) Angew Chem Int Ed Engl 43: 6735-6738


Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'
A, B
22Streptomyces paromomycinus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JS4
Query on JS4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		(2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-4-(2-(3-AMINOPROPYLAMINO)ETHOXY)-5-((1R,2R,3S,5R,6S)-3,5-DIAM INO-2-((2S,3R,4R,5S,6R)-3-AMINO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-( HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL
C28 H57 N7 O14
FJVLHNJZMYGVLT-XXJRHLBLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
JS4 PDBBind:  2BEE Kd: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.220 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.171α = 90
b = 39.171β = 90
c = 99.027γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-09
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy