Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF A NONPOLAR, NON HYDROGEN BONDED BASE PAIR SURROGATE IN DNA.
 
Authors :  E. T. Kool, T. R. Krugh, K. M. Guckian
Date :  01 Feb 00  (Deposition) - 16 Feb 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  1,2
Keywords :  Dna, Nonpolar, Isosteric, Dna Base Analogs (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. M. Guckian, T. R. Krugh, E. T. Kool
Solution Structure Of A Nonpolar, Non-Hydrogen-Bonded Base Pair Surrogate In Dna
J. Am. Chem. Soc. V. 122 6841 2000
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*CP*AP*TP*(DFT)P*GP*TP*TP*AP*CP*C)-3'
    Chains1
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*GP*TP*AP*AP*CP*(MBZ)P*AP*TP*GP*CP*G)-3'
    Chains2
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1DFT1Mod. Nucleotide1-[2-DEOXYRIBOFURANOSYL]-2,4-DIFLUORO-5-METHYL-BENZENE-5'MONOPHOSPHATE
2MBZ1Mod. Nucleotide1-[2-DEOXYRIBOFURANOSYL]-4-METHYL-BENZOIMIDAZOLE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1EEK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1EEK)

(-) Sequences/Alignments

NMR Structure
   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 1 from PDB  Type:DNA  Length:12
                                           
                  1eek 1  1 CGCATxGTTACC 12
                                 |  10  
                                 6-DFT  

Chain 2 from PDB  Type:DNA  Length:12
                                           
                  1eek 2  1 GGTAACxATGCG 12
                                  | 10  
                                  7-MBZ 

   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 1EEK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 1EEK)

 Visualization

(-) Interactive Views

NMR Structure
  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
    DFT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MBZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1eek)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1eek)
 

(-) 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
  1eek
    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 1EEK)

(-) Related Entries Specified in the PDB File

1bw7 SOLUTION STRUCTURE OF AN F - A PAIR