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 :  DNA WITH PYRENE PAIRED AT ABASIC SITE
 
Authors :  S. Smirnov, T. J. Matray, E. T. Kool, C. De Los Santos
Date :  04 Oct 00  (Deposition) - 18 Oct 00  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (8x)
Keywords :  Pyrene, Furan, Non-Polar Dna Pair (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Smirnov, T. J. Matray, E. T. Kool, C. De Los Santos
Integrity Of Duplex Structures Without Hydrogen Bonding: Dna With Pyrene Paired At Abasic Sites
Nucleic Acids Res. V. 30 5561 2002
PubMed-ID: 12490724  |  Reference-DOI: 10.1093/NAR/GKF688
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*AP*CP*AP*AP*AP*CP*AP*(PYP))-3'
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - 5'-D(*GP*TP*GP*CP*(3DR)P*TP*GP*TP*TP*TP*GP*TP*G)- 3'
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure (8x)

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2PYP1Mod. Nucleotide2'-DEOXYRIBOFURANOSYLPYRENE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1FZS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1FZS)

(-) 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 A from PDB  Type:DNA  Length:9
                                        
                  1fzs A  1 CACAAACAx  9
                                    |
                                    9-PYP

Chain B from PDB  Type:DNA  Length:13
                                            
                  1fzs B 14 GTGCxTGTTTGTG 26
                                |   23   
                                |        
                               18-3DR    

   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 1FZS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

 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
    3DR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PYP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1fzs)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1fzs)
 

(-) 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
  1fzs
    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 1FZS)

(-) Related Entries Specified in the PDB File

1fzl 1FZL CONTAINS A DNA DUPLEX WITH A PYRENE RESIDUE PAIRED AT AN ABASIC SITE