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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-ALLYL 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 :  15 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*(2AT)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  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
12AT2Mod. Nucleotide2'-O-ALLYL THYMIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1Y9F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y9F)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y9F)

(-) 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
                                         
                  1y9f A  1 GCGTAtACGC 10
                                 |  10
                                 6-2AT


Chain B from PDB  Type:DNA/RNA  Length:10
                                         
                  1y9f B 11 GCGTAtACGC 20
                                 |  20
                                16-2AT
   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 1Y9F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y9F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Y9F)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Y9F)

 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
    2AT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1y9f)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y9f)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1y9f
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP | HSSP
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB 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 Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Y9F)

(-) Related Entries Specified in the PDB File

1wv5 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, MG-FORM
1wv6 X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, SR-FORM
1y7f CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- [HYDROXY(METHYLENEAMINO)OXY]ETHYL] THYMIDINE (T*)
1y84 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- (IMIDAZOLYL)ETHYL] THYMIDINE (T*)
1y86 CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- (FLUORO)ETHYL] THYMIDINE (T*)
1y8l CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O-[2- (TRIFLUORO)ETHYL] THYMIDINE (T*)
1y8v CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O- PROPYL THYMIDINE (T*)
1y9s CRYSTAL STRUCTURE OF THE A-DNA GCGTAT*CGC WITH A 2'-O- PROPARGYL THYMIDINE (T*)