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(-) Description

Title :  CRYSTAL STRUCTURE OF D(GCGAGAGC): THE DNA QUADRUPLEX STRUCTURE SPLIT FROM THE OCTAPLEX
 
Authors :  J. Kondo, S. Umeda, T. Sunami, A. Takenaka
Date :  03 Nov 03  (Deposition) - 08 Jun 04  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Octaplex, Quadruplex, G-Duet, Base-Intercalated Duplex, Base- Intercalated Motif, Sheared G:A Pair, Dna, Deoxyribonucleic Acid, X- Ray Analysis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kondo, W. Adachi, S. Umeda, T. Sunami, A. Takenaka
Crystal Structures Of A Dna Octaplex With I-Motif Of G-Quartets And Its Splitting Into Two Quadruplexes Suggest Folding Mechanism Of Eight Tandem Repeats
Nucleic Acids Res. V. 32 2541 2004
PubMed-ID: 15133122  |  Reference-DOI: 10.1093/NAR/GKH575

(-) Compounds

Molecule 1 - 5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1C382Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1C384Mod. Nucleotide5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:5 , HOH A:25 , DG B:13BINDING SITE FOR RESIDUE K A 104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V3O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V3O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V3O)

(-) Exons   (0, 0)

(no "Exon" information available for 1V3O)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:DNA  Length:8
                                       
                  1v3o A  1 GcGAGAGC  8
                             |      
                             |      
                             2-C38  


Chain B from PDB  Type:DNA  Length:8
                                       
                  1v3o B  9 GcGAGAGC 16
                             |      
                            10-C38
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1V3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V3O)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1V3O)

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  1v3o
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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 1V3O)

(-) Related Entries Specified in the PDB File

1v3n THE SAME STRUCTURE, BR-DERIVATIVE
1v3p THE SAME STRUCTURE, I-DERIVATIVE, WITH I-MOTIF OF G-QUARTET