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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE COMPLEXED WITH AN AMPHIPHILIC PAROMOMYCIN O2''-ETHER ANALOGUE
 
Authors :  J. Szychowski, J. Kondo, O. Zahr, K. Auclair, E. Westhof, S. Hanessian, J. W. Keillor
Date :  20 May 11  (Deposition) - 21 Sep 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, Antibiotics, Ribosome, Decoding Site, Rna, Rna- Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Szychowski, J. Kondo, O. Zahr, K. Auclair, E. Westhof, S. Hanessian J. W. Keillor
Inhibition Of Aminoglycoside-Deactivating Enzymes Aph(3')-Iiia And Aac(6')-Ii By Amphiphilic Paromomycin O2''-Ether Analogues
Chemmedchem V. 6 1961 2011
PubMed-ID: 21905229  |  Reference-DOI: 10.1002/CMDC.201100346

(-) Compounds

Molecule 1 - RNA (5'- R(P*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, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1JS62Ligand/Ion(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-{[3-O-(2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSYL)-2-O-{2-[(2-PHENYLETHYL)AMINO]ETHYL}-BETA-D-RIBOFURANOSYL]OXY}-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE

(-) 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 , U B:25 , C B:26 , A B:27BINDING SITE FOR RESIDUE JS6 A 50
2AC2SOFTWAREG A:3 , U A:4 , C A:5 , A A:6 , G B:33 , U B:34 , G B:35 , A B:36 , A B:37 , G B:38 , U B:39BINDING SITE FOR RESIDUE JS6 B 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S4P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S4P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S4P)

(-) 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)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:RNA  Length:21
                                                    
                  3s4p A  1 GCGUCACACCGGUGAAGUCGC 21
                                    10        20 


Chain B from PDB  Type:RNA  Length:21
                                                    
                  3s4p B 22 GCGUCACACCGGUGAAGUCGC 42
                                    31        41
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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 3S4P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S4P)

(-) Pfam Domains  (0, 0)

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(-) 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

2be0 2bee 2pwt