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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2-(IMIDAZOLYL)ETHYL] THYMIDINE (T*)
 
Authors :  M. Egli, G. Minasov, V. Tereshko, P. S. Pallan, M. Teplova, G. B. Inamati, E. A. Lesnik, S. R. Owens, B. S. Ross, T. P. Prakash, M. Manoharan
Date :  10 Dec 04  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, A-Dna, O2'-Modification, Decamer. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Egli, G. Minasov, V. Tereshko, P. S. Pallan, M. Teplova, G. B. Inamati, E. A. Lesnik, S. R. Owens, B. S. Ross, T. P. Prakash, M. Manoharan
Probing The Influence Of Stereoelectronic Effects On The Biophysical Properties Of Oligonucleotides: Comprehensive Analysis Of The Rna Affinity, Nuclease Resistance, And Crystal Structure Of Ten 2'-O-Ribonucleic Acid Modifications.
Biochemistry V. 44 9045 2005
PubMed-ID: 15966728  |  Reference-DOI: 10.1021/BI050574M
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*TP*AP*(EIT)P*AP*CP*GP*C)-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  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EIT2Mod. Nucleotide((3R,4R,5R)-4-(2-(1H-IMIDAZOL-1-YL)ETHOXY)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SPM1Ligand/IonSPERMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDA A:5 , EIT A:6 , HOH A:122 , DG B:13 , DT B:14 , DC B:18 , DG B:19 , DC B:20 , HOH B:157 , HOH B:163BINDING SITE FOR RESIDUE SPM B 100
2AC2SOFTWAREHOH A:102 , HOH A:103 , HOH A:104 , HOH A:106 , HOH B:105 , HOH B:107BINDING SITE FOR RESIDUE MG A 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y84)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y84)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y84)

(-) 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/RNA  Length:10
                                         
                  1y84 A  1 GCGTAtACGC 10
                                 |  10
                                 6-EIT


Chain B from PDB  Type:DNA/RNA  Length:10
                                         
                  1y84 B 11 GCGTAtACGC 20
                                 |  20
                                16-EIT
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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 1Y84)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y84)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y84)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Y84)

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  1y84
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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

1y7f CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- [HYDROXY(METHYLENEAMINO)OXY]ETHYL] THYMIDINE (T*)
1y86 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- (FLUORO)ETHYL] THYMIDINE (T*)