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(-) Description

Title :  COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS5-39 AND THE 16S-RRNA A-SITE.
 
Authors :  B. Francois, E. Westhof
Date :  21 Oct 05  (Deposition) - 20 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna-Aminoglycoside Interactions, A Site, Uou Pairs, Aa Bulges (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Francois, J. Szychowski, S. S. Adhikari, K. Pachamuthu, E. E. Swayze, R. H. Griffey, M. T. Migawa, E. Westhof, S. Hanessian
Antibacterial Aminoglycosides With A Modified Mode Of Binding To The Ribosomal-Rna Decoding Site
Angew. Chem. Int. Ed. Engl. V. 43 6735 2004
PubMed-ID: 15593140  |  Reference-DOI: 10.1002/ANIE.200462092
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 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'
    Chains: A, B
    Engineered: YES
    Other Details: 16S RRNA A SITE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1JS52Ligand/Ion(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)-PIPERIDIN-3-YLMETHYLAMINO)ETHOXY)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:13 , G A:14 , A A:15 , A A:16 , G A:17 , U A:18 , HOH A:112 , HOH A:124 , HOH A:135 , C B:23 , U B:25 , C B:26 , A B:27 , A B:29BINDING SITE FOR RESIDUE JS5 A 50
2AC2SOFTWAREG A:3 , U A:4 , C A:5 , A A:6 , A A:8 , HOH A:126 , U B:34 , G B:35 , A B:36 , A B:37 , G B:38 , U B:39 , HOH B:107BINDING SITE FOR RESIDUE JS5 B 51

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:21
                                                    
                  2be0 A  1 GCGUCACACCGGUGAAGUCGC 21
                                    10        20 


Chain B from PDB  Type:RNA  Length:21
                                                    
                  2be0 B 22 GCGUCACACCGGUGAAGUCGC 42
                                    31        41
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1j7t CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PAROMOMYCIN AND THE 16S-RRNA A-SITE
2bee CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS4 AND THE 16S-RRNA A SITE
2esi CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN KANAMYCIN A AND THE 16S-RRNA A SITE
2esj CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN LIVIDOMYCIN A AND THE 16S-RRNA A SITE