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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PROKARYOTIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB30
 
Authors :  J. Kondo, M. Hainrichson, I. Nudelman, D. Shallom-Shezifi, T. Baasov, E. Westhof
Date :  02 Dec 06  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, Antibiotics, Ribosome, Decoding Site, Prokaryote, Translation Inhibition, Stop Codon Readthrough, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kondo, M. Hainrichson, I. Nudelman, D. Shallom-Shezifi, C. M. Barbieri, D. S. Pilch, E. Westhof, T. Baasov
Differential Selectivity Of Natural And Synthetic Aminoglycosides Towards The Eukaryotic And Prokaryotic Decoding A Sites.
Chembiochem V. 8 1700 2007
PubMed-ID: 17705310  |  Reference-DOI: 10.1002/CBIC.200700271
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (5'- R(*UP*UP*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: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1N301Ligand/Ion(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:5 , C A:7 , A A:8 , A A:17 , G B:39 , A B:40 , A B:41 , G B:42 , U B:43 , C B:44BINDING SITE FOR RESIDUE N30 B 1

(-) SS Bonds  (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:RNA  Length:21
                                                    
                  2o3x A  3 GCGUCACACCGGUGAAGUCGC 23
                                    12        22 


Chain B from PDB  Type:RNA  Length:21
                                                    
                  2o3x B 26 GCGUCACACCGGUGAAGUCGC 46
                                    35        45
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 Classification and Annotation

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

2o3v CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB33
2o3w CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMOMYCIN
2o3y CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMAMINE DERIVATIVE NB30