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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX RNA BOUND TO RIBOSTAMYCIN
 
Authors :  S. Freisz, K. Lang, R. Micura, P. Dumas, E. Ennifar
Date :  29 Jan 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Rna, Antibiotic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Freisz, K. Lang, R. Micura, P. Dumas, E. Ennifar
Binding Of Aminoglycoside Antibiotics To The Duplex Form Of The Hiv-1 Genomic Rna Dimerization Initiation Site.
Angew. Chem. Int. Ed. Engl. V. 47 4110 2008
PubMed-ID: 18435520  |  Reference-DOI: 10.1002/ANIE.200800726
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HIV-1 SUBTYPE F GENOMIC RNA
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1RIO2Ligand/IonRIBOSTAMYCIN
2UMS2Mod. Nucleotide2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:7 , A A:8 , A A:9 , G A:10 , U A:11 , HOH A:26 , HOH A:32 , HOH A:35 , HOH A:40 , HOH A:45 , HOH A:48 , HOH A:51 , HOH A:52 , HOH A:57 , HOH A:62 , HOH A:92 , A B:14 , C B:15 , A B:16 , HOH B:25 , HOH B:29 , HOH B:56 , HOH B:73BINDING SITE FOR RESIDUE RIO A 24
2AC2SOFTWAREC A:13 , A A:14 , C A:15 , A A:16 , G B:7 , A B:8 , A B:9 , G B:10 , U B:11 , G B:12 , HOH B:29 , HOH B:36 , HOH B:37 , HOH B:38 , HOH B:51 , HOH B:57 , HOH B:60 , HOH B:63 , HOH B:93 , HOH B:96BINDING SITE FOR RESIDUE RIO B 24

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C3Z)

(-) 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
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Chain A from PDB  Type:DNA/RNA  Length:23
                                                      
                  3c3z A  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              |                    
                              3-UMS                


Chain B from PDB  Type:DNA/RNA  Length:23
                                                      
                  3c3z B  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              3-UMS
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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)

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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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 Related Entries

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(-) Related Entries Specified in the PDB File

2qek FREE SUBTYPE F HIV-1 DIS EXTENDED DUPLEX RNA
3c44
3c5d