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(-) Description

Title :  HIV-1 DIS(MAL) DUPLEX PB-SOAKED
 
Authors :  E. Ennifar, P. Walter, P. Dumas
Date :  14 Dec 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rna, Hiv-1, Metal Ions, Bulge (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Ennifar, P. Walter, P. Dumas
A Crystallographic Study Of The Binding Of 13 Metal Ions To Two Related Rna Duplexes
Nucleic Acids Res. V. 31 2671 2003
PubMed-ID: 12736317  |  Reference-DOI: 10.1093/NAR/GKG350
(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
    Other Details: HIV-1 DIS RNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MG10Ligand/IonMAGNESIUM ION
2PB3Ligand/IonLEAD (II) ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREG A:9 , G A:10 , A B:8 , G B:9BINDING SITE FOR RESIDUE PB B 31
02AC2SOFTWAREU A:3 , G A:4 , MG A:40 , MG B:41BINDING SITE FOR RESIDUE MG A 32
03AC3SOFTWAREU B:3 , G B:4BINDING SITE FOR RESIDUE MG B 33
04AC4SOFTWAREU B:6 , G B:7 , HOH B:116BINDING SITE FOR RESIDUE MG B 34
05AC5SOFTWAREA B:8 , G B:9BINDING SITE FOR RESIDUE PB B 35
06AC6SOFTWAREA A:8 , G A:9BINDING SITE FOR RESIDUE PB A 36
07AC7SOFTWAREG A:12BINDING SITE FOR RESIDUE MG A 37
08AC8SOFTWAREC A:1BINDING SITE FOR RESIDUE MG A 38
09AC9SOFTWAREG A:4 , MG A:32BINDING SITE FOR RESIDUE MG A 40
10BC1SOFTWAREMG A:32BINDING SITE FOR RESIDUE MG B 41
11BC2SOFTWAREG A:19BINDING SITE FOR RESIDUE MG A 43

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y95)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y95)

(-) 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
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Chain A from PDB  Type:RNA  Length:23
                                                      
                  1y95 A  1 CUUGCUGAGGUGCACACAGCAAG 23
                                    10        20   


Chain B from PDB  Type:RNA  Length:23
                                                      
                  1y95 B  1 CUUGCUGAGGUGCACACAGCAAG 23
                                    10        20
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 1Y95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y95)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Y95)

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  1y95
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1Y95)

(-) Related Entries Specified in the PDB File

1nlc HIV-1 DIS(MAL) DUPLEX ZN-SOAKED
1o3z HIV-1 DIS(MAL) DUPLEX RU HEXAMINE--SOAKED
1xp7 HIV-1 DIS(MAL) DUPLEX RUHEXA-SOAKED
1y6s HIV-1 DIS(MAL) DUPLEX BA-SOAKED
1y6t HIV-1 DIS(MAL) DUPLEX COHEXA-SOAKED
1y73 HIV-1 DIS(MAL) DUPLEX PTCL4-SOAKED
1y90 HIV-1 DIS(MAL) DUPLEX MN-SOAKED