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(-) Description

Title :  CRYSTAL STRUCTURE OF D(CGCGAATXCGCG) WHERE X IS 5-(N-AMINOHEXYL)CARBAMOYL-2'-DEOXYURIDINE
 
Authors :  E. C. M. Juan, J. Kondo, T. Kurihara, T. Ito, Y. Ueno, A. Matsuda, A. Takenaka
Date :  08 May 06  (Deposition) - 17 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Modified Nucleotide, 5-(N-Aminohexyl)Carbamoyl-2'- Deoxyuridine, B-Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. C. M. Juan, J. Kondo, T. Kurihara, T. Ito, Y. Ueno, A. Matsuda, A. Takenaka
Crystal Structures Of Dna:Dna And Dna:Rna Duplexes Containing 5-(N-Aminohexyl)Carbamoyl-Modified Uracils Reveal The Basis For Properties As Antigene And Antisense Molecules
Nucleic Acids Res. V. 35 1969 2007
PubMed-ID: 17341465  |  Reference-DOI: 10.1093/NAR/GKL821
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*DCP*DGP*DCP*DGP*DAP*DAP*DTP*DUP*DCP*DGP*DCP*DG)-3')
    Chains: A, B
    Engineered: YES
    Other Details: THIS DNA DODECAMER IS A SYNTHETIC CONSTRUCT.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CMY2Ligand/Ion(6-AMINOHEXYL)CARBAMIC ACID
2DU2Mod. Residue
3K1Ligand/IonPOTASSIUM ION
4MG1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:111 , HOH A:112 , HOH A:117 , HOH A:118 , HOH A:119 , HOH A:125BINDING SITE FOR RESIDUE MG A 13
2AC2SOFTWAREDT A:7 , DU A:8 , DT B:19 , DU B:20 , HOH B:124 , HOH B:128 , HOH B:187BINDING SITE FOR RESIDUE K B 2
3AC3SOFTWAREDC A:1 , DT A:7 , DU A:8 , HOH A:192 , DC B:15 , DG B:16 , DG B:24 , HOH B:125 , HOH B:134 , HOH B:152BINDING SITE FOR RESIDUE CMY A 108
4AC4SOFTWAREDT B:19 , DU B:20 , HOH B:130 , HOH B:204BINDING SITE FOR RESIDUE CMY B 120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DP7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DP7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DP7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DP7)

(-) Exons   (0, 0)

(no "Exon" information available for 2DP7)

(-) 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:DNA  Length:12
                                           
                  2dp7 A  1 CGCGAATxCGCG 12
                                   |10  
                                   8-DU 


Chain B from PDB  Type:DNA  Length:12
                                           
                  2dp7 B 13 CGCGAATxCGCG 24
                                   |22  
                                  20-DU
   Legend:   → Mismatch (orange background)
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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 2DP7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DP7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DP7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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(-) Related Entries Specified in the PDB File

2dpb 2dpc