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(-) Description

Title :  COMPLEX BETWEEN LIVIDOMYCIN A AND THE 16S-RRNA A SITE
 
Authors :  E. Westhof
Date :  26 Oct 05  (Deposition) - 20 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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, R. J. M. Russel, J. B. Murray, F. Aboul-Ela, B. Masquida, Q. Vicens, E. Westhof
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. V. 33 5677 2005
PubMed-ID: 16214802  |  Reference-DOI: 10.1093/NAR/GKI862
(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: BACTERIAL 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
1LIV2Ligand/Ion(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREU A:14 , G A:15 , A A:17 , G A:18 , U A:19 , HOH A:101 , HOH A:117 , C B:26 , G B:27 , C B:29 , A B:30 , HOH B:100BINDING SITE FOR RESIDUE LIV A 50
2AC2SOFTWAREC A:3 , G A:4 , U A:5 , C A:6 , A A:7 , C A:20 , U B:37 , G B:38 , A B:39 , A B:40 , G B:41 , U B:42 , HOH B:105 , HOH B:113 , HOH B:124 , HOH B:128 , HOH B:129 , HOH B:130 , HOH B:137 , HOH B:143 , HOH B:170 , HOH B:189BINDING SITE FOR RESIDUE LIV B 51

(-) SS Bonds  (0, 0)

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

(-) 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)

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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
                                                    
                  2esj A  2 GCGUCACACCGGUGAAGUCGC 22
                                    11        21 


Chain B from PDB  Type:RNA  Length:21
                                                    
                  2esj B 25 GCGUCACACCGGUGAAGUCGC 45
                                    34        44
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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 2ESJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ESJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ESJ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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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 COMPLEX BETWEEN NATURAL PAROMOMYCIN AND 16S RRNA A SITE
2be0 COMPLEX BETWEEN PAROMOMYCIN DERIVATIVE JS5-39 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