Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) 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'
    ChainsA, B
    EngineeredYES
    SyntheticYES

 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
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

   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 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)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y84)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y84
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP | HSSP
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Y84)

(-) 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*)