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(-) Description

Title :  HIV-1 SUBTYPE A GENOMIC RNA DIMERIZATION INITIATION SITE
 
Authors :  E. Ennifar, P. Dumas
Date :  08 Oct 04  (Deposition) - 18 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna, Loop-Loop Complex, Hiv-1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ennifar, P. Dumas
Polymorphism Of Bulged-Out Residues In Hiv-1 Rna Dis Kissing Complex And Structure Comparison With Solution Studies
J. Mol. Biol. V. 356 771 2006
PubMed-ID: 16403527  |  Reference-DOI: 10.1016/J.JMB.2005.12.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP *CP*AP*AP*G)-3'
    Chains: A, B
    Engineered: YES
    Synonym: HIV-1 GENOMIC RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NA1Ligand/IonSODIUM ION
3SO43Ligand/IonSULFATE ION
4SPM1Ligand/IonSPERMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:146 , C B:1 , HOH B:136BINDING SITE FOR RESIDUE SO4 B 101
2AC2SOFTWAREA A:8 , G A:9 , HOH A:134 , HOH A:144 , A B:8BINDING SITE FOR RESIDUE SO4 A 102
3AC3SOFTWAREC A:1 , U A:2BINDING SITE FOR RESIDUE NA A 105
4AC4SOFTWAREC A:1BINDING SITE FOR RESIDUE SO4 A 106
5AC5SOFTWAREG A:12BINDING SITE FOR RESIDUE MG A 107
6AC6SOFTWAREG A:9 , G A:10 , U A:11 , HOH A:110 , HOH A:124 , HOH A:138 , G B:10 , HOH B:119BINDING SITE FOR RESIDUE SPM A 108

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XPF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XPF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XPF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XPF)

(-) Exons   (0, 0)

(no "Exon" information available for 1XPF)

(-) 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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:RNA  Length:23
                                                      
                  1xpf A  1 CUUGCUGAGGUGCACACAGCAAG 23
                                    10        20   


Chain B from PDB  Type:RNA  Length:23
                                                      
                  1xpf B  1 CUUGCUGAGGUGCACACAGCAAG 23
                                    10        20
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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 1XPF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XPF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XPF)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

1jjm
1jjn
1k9w
1xp7 HIV-1 SUBTYPE F
1xpe HIV-1 SUBTYPE B