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PDBsum entry 2be0
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dna_rna ligands links
RNA/antibiotic PDB id
2be0

 

 

 

 

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Contents
DNA/RNA
Ligands
JS5 ×2
Waters ×44
PDB id:
2be0
Name: RNA/antibiotic
Title: Complex between paromomycin derivative js5-39 and the 16s-rrna a-site.
Structure: 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'. Chain: a, b. Engineered: yes. Other_details: 16s rrna a site
Source: Synthetic: yes. Streptomyces rimosus subsp. Paromomycinus. Organism_taxid: 92743
Biol. unit: Dimer (from PQS)
Resolution:
2.63Å     R-factor:   0.224     R-free:   0.267
Authors: B.Francois,E.Westhof
Key ref: B.François et al. (2004). Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site. Angew Chem Int Ed Engl, 43, 6735-6738. PubMed id: 15593140
Date:
21-Oct-05     Release date:   20-Dec-05    
 Headers
 References

DNA/RNA chains
  G-C-G-U-C-A-C-A-C-C-G-G-U-G-A-A-G-U-C-G-C 21 bases
  G-C-G-U-C-A-C-A-C-C-G-G-U-G-A-A-G-U-C-G-C 21 bases

 

 
Angew Chem Int Ed Engl 43:6735-6738 (2004)
PubMed id: 15593140  
 
 
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site.
B.François, J.Szychowski, S.S.Adhikari, K.Pachamuthu, E.E.Swayze, R.H.Griffey, M.T.Migawa, E.Westhof, S.Hanessian.
 
  ABSTRACT  
 

 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20056889 M.H.Bailor, X.Sun, and H.M.Al-Hashimi (2010).
Topology links RNA secondary structure with global conformation, dynamics, and adaptation.
  Science, 327, 202-206.  
18346970 J.Kondo, and E.Westhof (2008).
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
  Nucleic Acids Res, 36, 2654-2666.
PDB codes: 3bnl 3bnn 3bno 3bnp 3bnq 3bnr 3bns 3bnt
18174989 M.Hainrichson, I.Nudelman, and T.Baasov (2008).
Designer aminoglycosides: the race to develop improved antibiotics and compounds for the treatment of human genetic diseases.
  Org Biomol Chem, 6, 227-239.  
17722211 J.Kondo, K.Pachamuthu, B.François, J.Szychowski, S.Hanessian, and E.Westhof (2007).
Crystal Structure of the Bacterial Ribosomal Decoding Site Complexed with a Synthetic Doubly Functionalized Paromomycin Derivative: a New Specific Binding Mode to an A-Minor Motif Enhances in vitro Antibacterial Activity.
  ChemMedChem, 2, 1631-1638.
PDB code: 2pwt
17705310 J.Kondo, M.Hainrichson, I.Nudelman, D.Shallom-Shezifi, C.M.Barbieri, D.S.Pilch, E.Westhof, and T.Baasov (2007).
Differential selectivity of natural and synthetic aminoglycosides towards the eukaryotic and prokaryotic decoding A sites.
  Chembiochem, 8, 1700-1709.
PDB codes: 2o3v 2o3w 2o3x 2o3y
17505105 J.Kondo, T.Sunami, and A.Takénaka (2007).
The structure of a d(gcGAACgc) duplex containing two consecutive bulged A residues in both strands suggests a molecular switch.
  Acta Crystallogr D Biol Crystallogr, 63, 673-681.
PDB code: 2got
16892199 J.Zhou, G.Wang, L.H.Zhang, and X.S.Ye (2007).
Modifications of aminoglycoside antibiotics targeting RNA.
  Med Res Rev, 27, 279-316.  
16452297 J.Kondo, A.Urzhumtsev, and E.Westhof (2006).
Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.
  Nucleic Acids Res, 34, 676-685.
PDB code: 2fqn
16915600 K.F.Blount, and Y.Tor (2006).
A tale of two targets: differential RNA selectivity of nucleobase-aminoglycoside conjugates.
  Chembiochem, 7, 1612-1621.  
16408312 M.Kaiser, M.Sainlos, J.M.Lehn, S.Bombard, and M.P.Teulade-Fichou (2006).
Aminoglycoside-quinacridine conjugates: towards recognition of the P6.1 element of telomerase RNA.
  Chembiochem, 7, 321-329.  
16214802 B.François, R.J.Russell, J.B.Murray, F.Aboul-ela, B.Masquida, Q.Vicens, and E.Westhof (2005).
Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding.
  Nucleic Acids Res, 33, 5677-5690.
PDB codes: 2esi 2esj 2et3 2et4 2et5 2et8
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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