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(-) Description

Title :  1.5 A X-RAY CRYSTAL STRUCTURE OF APRAMYCIN COMPLEX WITH RNA FRAGMENT GGCGUCGCUAGUACCG/GGUACUAAAAGUCGCCC CONTAINING THE HUMAN RIBOSOMAL DECODING A SITE: RNA CONSTRUCT WITH 3'-OVERHANG
 
Authors :  T. Hermann, V. Tereshko, E. Skripkin, D. J. Patel
Date :  28 Dec 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside Antibiotics, Apramycin, Ribosomal Decoding Site, A Site, Homo Sapiens, Rna Duplex, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Hermann, V. Tereshko, E. Skripkin, D. J. Patel
Apramycin Recognition By The Human Ribosomal Decoding Site.
Blood Cells Mol. Dis. V. 38 193 2007
PubMed-ID: 17258916  |  Reference-DOI: 10.1016/J.BCMD.2006.11.006

(-) Compounds

Molecule 1 - RNA (5'-R(*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*CP*G)- 3')
    ChainsA
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES
 
Molecule 2 - RNA (5'- R(*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*CP*C)-3')
    ChainsB
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1AM21Ligand/IonAPRAMYCIN
2MG2Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESO4 A:102 , HOH A:130 , HOH A:143 , HOH A:200 , G A:1408 , C A:1409 , U A:1410 , A A:1411 , G A:1412 , U A:1413 , G B:84 , G B:85 , U B:86 , C B:100 , HOH B:118 , HOH B:119 , HOH B:131 , HOH B:134 , HOH B:157 , HOH B:170 , HOH B:194 , A B:1487 , C B:1488 , U B:1489BINDING SITE FOR RESIDUE AM2 B 101
2AC2SOFTWAREC A:16 , G A:17 , HOH A:111 , HOH A:149 , G B:84 , C B:99 , C B:100 , AM2 B:101BINDING SITE FOR RESIDUE SO4 A 102
3AC3SOFTWAREHOH A:109 , HOH B:105 , HOH B:106 , HOH B:107 , HOH B:108 , HOH B:110BINDING SITE FOR RESIDUE MG B 103
4AC4SOFTWAREHOH A:111 , HOH A:112 , HOH A:113 , HOH A:114 , HOH A:115 , HOH A:116BINDING SITE FOR RESIDUE MG A 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OE5)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OE5)

(-) Exons   (0, 0)

(no "Exon" information available for 2OE5)

(-) 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:16
                                                 
                2oe5 A    2 GGCGUCGCUAGUACCG   17
                             ||   1411 ||   
                             3|     1413|   
                           1404        14   

Chain B from PDB  Type:RNA  Length:17
                                                  
                2oe5 B   84 GGUACUAAAAGUCGCCC  100
                              ||  1493   ||  
                             86|      1497|  
                            1487         98  

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2OE5)

(-) 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

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(-) Related Entries Specified in the PDB File

2oe6 2.4 A X-RAY CRYSTAL STRUCTURE OF UNLIGANDED RNA FRAGMENT GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC CONTAINING THE HUMAN RIBOSOMAL DECODING A SITE: RNA CONSTRUCT WITH 5'-OVERHANG
2oe8 1.8 A X-RAY CRYSTAL STRUCTURE OF APRAMYCIN COMPLEX WITH RNA FRAGMENT GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC CONTAINING THE HUMAN RIBOSOMAL DECODING A SITE: RNA CONSTRUCT WITH 5'- OVERHANG