Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theoretical Model
collapse expand < >
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  DNA QUADRUPLEX STRUCTURE, (12MER) DNA, THEORETICAL MODEL
 
Authors :  V. M. Marathias, K. Y. Wang, S. Kumar, S. Swaminathan, P. H. Bolton
Date :  11 Apr 96  (Deposition) - 08 Nov 96  (Release) - 08 Nov 96  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,B,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Qudraplex Dna, Mn Binding Dna, Non-Thrombin Inhibitor, Telomere Dna Duplex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Marathias, K. Y. Wang, S. Kumar, S. Swaminathan, P. H. Bolton
Determination Of The Number And Location Of The Manganese Binding Sites Of Dna Quadraplexes In Solution By Epr And Nmr In The Prescence And Absence Of Thrombin
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (12MER, D(GGGGTTTTGGG))
    Chains: A, B
    Engineered: YES
    Other Details: PREDICTED STRUCTURE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Theoretical Model (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (0, 0)

(no "Site" information available for 1QDJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QDJ)

(-) Sequences/Alignments

Theoretical Model
   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  Length:12
                                           
                  1qdj A  1 GGGGTTTTGGGG 12
                                    10  


Chain B from PDB  Type:DNA  Length:12
                                           
                  1qdj B  1 GGGGTTTTGGGG 12
                                    10
   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 1QDJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Theoretical Model(hide GO term definitions)
    (no "Gene Ontology" information available for 1QDJ)

 Visualization

(-) Interactive Views

Theoretical Model
  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
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1qdj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qdj)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Theoretical Model 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
  1qdj
    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 1QDJ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QDJ)