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(-) Description

Title :  THE DICKERSON-DREW B-DNA DODECAMER REVISITED-AT ATOMIC RESOLUTION
 
Authors :  V. Tereshko, G. Minasov, M. Egli
Date :  12 Nov 98  (Deposition) - 25 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  B-Dna Dodecamer, High Resolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Tereshko, G. Minasov, M. Egli
The Dickerson-Drew B-Dna Dodecamer Revisited-At Atomic Resolution
J. Am. Chem. Soc. V. 121 470 1999
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*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, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2TAF2Mod. Nucleotide2'-DEOXY-2'-FLUORO-ARABINO-FURANOSYL THYMINE-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:26 , HOH A:28 , HOH B:27 , HOH B:29 , HOH B:30 , HOH B:31BINDING SITE FOR RESIDUE MG A 25
2AC2SOFTWARETAF B:19 , HOH B:33 , HOH B:34 , HOH B:35 , HOH B:36 , HOH B:37BINDING SITE FOR RESIDUE MG B 32
3AC3SOFTWAREHOH A:40 , HOH A:43 , HOH B:39 , HOH B:41 , HOH B:42 , HOH B:44BINDING SITE FOR RESIDUE MG B 38
4AC4SOFTWAREDA B:17 , HOH B:46 , HOH B:47 , HOH B:48 , HOH B:49 , HOH B:50BINDING SITE FOR RESIDUE MG B 45
5AC5SOFTWAREHOH A:52 , HOH A:53 , HOH A:54 , HOH A:55 , HOH A:122 , HOH A:179BINDING SITE FOR RESIDUE MG A 51

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 436D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 436D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 436D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 436D)

(-) Exons   (0, 0)

(no "Exon" information available for 436D)

(-) 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
                                           
                  436d A  1 CGCGAAtTCGCG 12
                                  | 10  
                                  7-TAF 


Chain B from PDB  Type:DNA  Length:12
                                           
                  436d B 13 CGCGAAtTCGCG 24
                                  | 22  
                                 19-TAF
   Legend:   → Mismatch (orange background)
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  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 436D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 436D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 436D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 436D)

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  Cis Peptide Bonds
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  436d
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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

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