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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACTERIAL RIBOSOMAL DECODING SITE IN COMPLEX WITH 4'-DEOXY-4'-FLUORO NEOMYCIN ANALOG
 
Authors :  S. Hanessian, O. M. Saavedra, M. A. Vilchis-Reyes, J. P. Maianti, H. Kan P. Dozzo, L. A. Feeney, E. S. Armstrong, J. Kondo
Date :  21 Apr 14  (Deposition) - 07 Jan 15  (Release) - 07 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribosome, Aminoglycoside, Rna-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hanessian, O. M. Saavedra, M. A. Vilchis-Reyes, J. P. Maianti, H. Kanazawa, P. Dozzo, R. D. Matias, A. Serio, J. Kondo
Synthesis, Broad Spectrum Antibacterial Activity, And X-Ray Co-Crystal Structure Of The Decoding Bacterial Ribosomal A-Site With 4'-Deoxy-4'-Fluoro Neomycin Analogs
Chem Sci V. 5 4621 2014
PubMed: search  |  Reference-DOI: 10.1039/C4SC01626B

(-) Compounds

Molecule 1 - RNA (5'- *UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C- 3')
    Chains: A, B
    Engineered: YES
    Organism Scientific: SYNTHETIC
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NMZ1Ligand/Ion(2S)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-3-{[3-O-(2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPYRANOSYL)-BETA-D-RIBOFURANOSYL]OXY}-4-[(2,6-DIAMINO-2,4,6-TRIDEOXY-4-FLUORO-ALPHA-D-GALACTOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:13binding site for residue MG A 101
2AC2SOFTWAREG A:3 , C A:4 , G A:5 , U A:6 , C A:7 , A A:8 , C A:9 , G B:37 , C B:38 , G B:39 , A B:40 , A B:41 , G B:42 , U B:43 , C B:44 , G B:45 , C B:46binding site for residue NMZ B 101

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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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:23
                                                      
                  4pdq A  1 UUGCGUCACGCCGGCGAAGUCGC 23
                                    10        20   


Chain B from PDB  Type:RNA  Length:23
                                                      
                  4pdq B 24 UUGCGUCACGCCGGCGAAGUCGC 46
                                    33        43
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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