2BE0

Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
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 22N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JS5
Query on JS5

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)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R,4R,5S,6R)-3-AMINO-4 ,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-(HYDROXYMETHYL)-4-(2-((R)-PIPERIDI N-3-YLMETHYLAMINO)ETHOXY)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL
C31 H61 N7 O14
AHJDGUQMOYBKDU-NSCPTEJBSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JS5 PDBBind:  2BE0 Kd: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.141α = 90
b = 39.141β = 90
c = 99.14γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



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