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(-) Description

Title :  RNA-BINDING AFFINITIES AND CRYSTAL STRUCTURE OF OLIGONUCLEOTIDES CONTAINING FIVE-ATOM AMIDE-BASED BACKBONE STRUCTURES
 
Authors :  P. S. Pallan, M. Egli
Date :  01 May 06  (Deposition) - 01 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna:Rna Hybrid, Amide Bearing Dna, Thymidine Dimers, Internucleosidic Amide Linkage, Dna, Rna, Dna/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Pallan, P. Von Matt, C. J. Wilds, K. -H. Altmann, M. Egli
Rna-Binding Affinities And Crystal Structure Of Oligonucleotides Containing Five-Atom Amide-Based Backbone Structures.
Biochemistry V. 45 8048 2006
PubMed-ID: 16800629  |  Reference-DOI: 10.1021/BI060354O
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*TP*TP*CP*(T2T)P*(CBR)P*TP*TP*C)-3'
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'
    Chains: 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  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
13CO2Ligand/IonCOBALT (III) ION
2CBR1Mod. Nucleotide5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3SPM1Ligand/IonSPERMINE
4T2T1Mod. Nucleotide[(2S,3S,5R)-3-[(2S)-3-({[(2R,3S,4R,5R)-3-HYDROXY-4-METHOXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL}AMINO)-2-METHYL-3-OXOPROPYL]-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYLDIHYDROGEN PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECBR A:6 , DT A:8 , DC A:9 , A B:15BINDING SITE FOR RESIDUE SPM B 521

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GUN)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:DNA/RNA  Length:8
                                       
                  2gun A  1 TTCxcTTC  9
                               ||   
                               ||   
                               4-T2T
                                6-CBR


Chain B from PDB  Type:RNA  Length:9
                                        
                  2gun B 10 GAAGAAGAA 18
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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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