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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A-DNA HEXAMER GGCGM5CC
 
Authors :  J. M. Vargason, B. F. Eichman, P. S. Ho
Date :  21 Jun 00  (Deposition) - 28 Aug 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  A-Dna, E-Dna, Double Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Vargason, B. F. Eichman, P. S. Ho
The Extended And Eccentric E-Dna Structure Induced By Cytosine Methylation Or Bromination.
Nat. Struct. Biol. V. 7 758 2000
PubMed-ID: 10966645  |  Reference-DOI: 10.1038/78985
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*GP*CP*GP*(5CM)P*C)-3')
    ChainsA, B, C, D, E, F
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
15CM6Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1F6E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F6E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F6E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F6E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F6E)

(-) Exons   (0, 0)

(no "Exon" information available for 1F6E)

(-) Sequences/Alignments

Asymmetric 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:6
                                     
                  1f6e A  1 GGCGcC  6
                                | 
                                | 
                                5-5CM

Chain B from PDB  Type:DNA  Length:6
                                     
                  1f6e B  7 GGCGcC 12
                                | 
                                | 
                               11-5CM

Chain C from PDB  Type:DNA  Length:6
                                     
                  1f6e C 13 GGCGcC 18
                                | 
                                | 
                               17-5CM

Chain D from PDB  Type:DNA  Length:6
                                     
                  1f6e D 19 GGCGcC 24
                                | 
                                | 
                               23-5CM

Chain E from PDB  Type:DNA  Length:6
                                     
                  1f6e E 25 GGCGcC 30
                                | 
                                | 
                               29-5CM

Chain F from PDB  Type:DNA  Length:6
                                     
                  1f6e F 31 GGCGcC 36
                                | 
                                | 
                               35-5CM

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 1F6E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1F6E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F6E)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1F6E)

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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 1F6E)

(-) Related Entries Specified in the PDB File

1f69 B-DNA HEXAMER GGCGCC WITH COBALT HEXAMINE
1f6c B-DNA HEXAMER GGCGCC WITH SPERMINE
1f6i E-DNA HEXAMER GGCGM5CC
1f6j E-DNA HEXAMER GGCGBR5CC