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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB33
 
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 :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, Antibiotics, Ribosome, Decoding Site, Homo Sapiens, Eukaryote, Cytoplasmic, 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*GP*CP*UP*CP*CP*GP*GP*AP*AP*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
1N331Ligand/Ion(2S,3R,4R,5S,6R)-3-AMINO-4-({[(2S,3R,4R,5S,6R)-3-AMINO-2-{[(1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}METHOXY)-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2,5-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREA A:16 , A A:17 , A A:18 , G A:19 , G B:28 , C B:30 , G B:31BINDING SITE FOR RESIDUE N33 A 50

(-) SS Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:RNA  Length:22
                                                     
                  2o3v A  2 UGCGUCGCUCCGGAAAAGUCGC 23
                                    11        21  


Chain B from PDB  Type:RNA  Length:21
                                                    
                  2o3v B 26 GCGUCGCUCCGGAAAAGUCGC 46
                                    35        45
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2O3V)

(-) CATH Domains  (0, 0)

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(-) Pfam 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

2fqn HOMO SAPIENS CYTOPLASMIC A SITE WITHOUT ANY AMINOGLYCOSIDES (CYTO-FREE)
2g5k HOMO SAPIENS CYTOPLASMIC A SITE COMPLEXED WITH APRAMYCIN (CYTO/APRAMYCIN)
2o3w CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMOMYCIN
2o3x CRYSTAL STRUCTURE OF THE PROKARYOTIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB30
2o3y CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMAMINE DERIVATIVE NB30