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(-) Description

Title :  CRYSTAL STRUCTURE OF A DNA DUPLEX CONTAINING 7,8-DIHYDROPYRIDOL[2,3-D]PYRIMIDIN-2-ONE
 
Authors :  A. Takenaka, E. C. M. Juan, S. Shimizu, T. Haraguchi, M. Xiao, T. Kurose, A. Ohkubo, M. Sekine, T. Shibata, C. L. Millington, D. M. Williams
Date :  09 Mar 09  (Deposition) - 31 Mar 10  (Release) - 31 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna, Duplex, Bicyclic Cytosine, 7, 8-Dihydropyridol[2, 3- D]Pyrimidin-2-One (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Takenaka, E. C. M. Juan, S. Shimizu, T. Haraguchi, M. Xiao, T. Kurose, A. Ohkubo, M. Sekine, T. Shibata, M. Millington
Insights Into The Stabilizing Contributions Of Bicyclic Cytosine Analogues: Crystal Structures Of Dna Duplexes Containing 7, 8-Dihydropyridol[2, 3-D]Pyrimidin-2-One
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*TP*(B7C)P*CP*GP*CP*G)-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
1B7C2Mod. Nucleotide3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-7,8-DIHYDROPYRIDO[2,3-D]PYRIMIDIN-2(3H)-ONE
2HT1Ligand/Ion2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:6 , DT A:7 , B7C A:8 , DC A:9 , DA B:18 , DT B:19 , B7C B:20 , DC B:21 , DG B:22BINDING SITE FOR RESIDUE HT B 25

(-) SS Bonds  (0, 0)

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

(-) 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)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:DNA  Length:12
                                           
                  3gjj A  1 CGCGAATcCGCG 12
                                   |10  
                                   8-B7C


Chain B from PDB  Type:DNA  Length:12
                                           
                  3gjj B 13 CGCGAATcCGCG 24
                                   |22  
                                  20-B7C
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GJJ)

(-) 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

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

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(-) Related Entries Specified in the PDB File

3gjh 3gjk 3gjl