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(-) Description

Title :  CRYSTAL STRUCTURE OF HIV-1 SUBTYPE F DIS EXTENDED DUPLEX RNA BOUND TO LIVIDOMYCIN
 
Authors :  S. Freisz, K. Lang, R. Micura, P. Dumas, E. Ennifar
Date :  31 Jan 08  (Deposition) - 06 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Rna, Aminoglycoside, Lividomycin, Extended Duplex (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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
2LIV2Ligand/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
3UMS2Mod. Nucleotide2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:73 , HOH B:30 , HOH B:35 , HOH B:39 , HOH B:43 , HOH B:44 , HOH B:58 , HOH B:62 , HOH B:74 , HOH B:86 , HOH B:95 , HOH B:104 , HOH B:105BINDING SITE FOR RESIDUE LIV B 24
2AC2SOFTWAREHOH A:30 , HOH A:33 , HOH B:27 , HOH B:30 , HOH B:31 , HOH B:35 , HOH B:43 , HOH B:45 , HOH B:65 , HOH B:85 , HOH B:88 , HOH B:90 , HOH B:111 , HOH B:112 , HOH B:113BINDING SITE FOR RESIDUE LIV B 25
3AC3SOFTWAREHOH A:39BINDING SITE FOR RESIDUE K B 26
4AC4SOFTWAREHOH A:74BINDING SITE FOR RESIDUE K A 24

(-) 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
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA/RNA  Length:23
                                                      
                  3c5d A  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              |                    
                              3-UMS                


Chain B from PDB  Type:DNA/RNA  Length:23
                                                      
                  3c5d B  1 CUxGCUGAAGUGCACACAGCAAG 23
                              |     10        20   
                              3-UMS
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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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(-) Related Entries Specified in the PDB File

2qek FREE SUBTYPE F HIV-1 DIS EXTENDED DUPLEX
3c3z SUBTYPE F HIV-1 DIS EXTENDED DUPLEX BOUND TO RIBOSTAMYCIN
3c44 SUBTYPE F HIV-1 DIS EXTENDED DUPLEX BOUND TO PAROMOMYCIN