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(-) Description

Title :  VINYL CARBOCYCLIC LNA
 
Authors :  P. R. Seth, C. A. Allerson, A. Berdeja, A. Siwkowski, P. S. Pallan, H. Gau T. P. Prakash, A. T. Watt, M. Egli, E. E. Swayze
Date :  24 Sep 10  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A,B
Keywords :  A-Form Dna, Vinyl Carbocyclic Lna, Antisense Oligonucleotides, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. P. Seth, C. R. Allerson, A. Berdeja, A. Siwkowski, P. S. Pallan, H. Gaus, T. P. Prakash, A. T. Watt, M. Egli, E. E. Swayze
An Exocyclic Methylene Group Acts As A Bioisostere Of The 2'-Oxygen Atom In Lna.
J. Am. Chem. Soc. V. 132 14942 2010
PubMed-ID: 20886816  |  Reference-DOI: 10.1021/JA105875E

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*GP*TP*AP*(UVX)P*AP*CP*GP*C)-3')
    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, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2UVX2Mod. Nucleotide[(1R,3R,4R,7S)-3-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-7-HYDROXY-5-METHYLIDENE-2-OXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:41 , DG A:101 , HOH B:31 , UVX B:206 , DA B:207BINDING SITE FOR RESIDUE MPD A 211

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OZ3)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:DNA  Length:10
                                          
                 3oz3 A 101 GCGTAxACGC 110
                                 | 110
                                 |    
                               106-UVX


Chain B from PDB  Type:DNA  Length:10
                                          
                 3oz3 B 201 GCGTAxACGC 210
                                 | 210
                               206-UVX
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3OZ3)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) 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

3oz4 3oz5