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

(-) Description

Title :  HIGH RESOLUTION NMR STRUCTURE OF THE STEREOREGULAR (ALL-RP)-PHOSPHOROTHIOATE-DNA/RNA HYBRID D (G*PS*C*PS*G*PS*T*PS*C*PS*A*PS*G*PS*G)R(CCUGACGC), MINIMIZED AVERAGE STRUCTURE
 
Authors :  M. Bachelin, G. Hessler, G. Kurz, J. G. Hacia, P. B. Dervan, H. Kessler
Date :  13 Oct 97  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B
Keywords :  Oligonucleotide, Dna-Rna Hybrid, Phosphorothioate, Thionucleotide, Antisense (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bachelin, G. Hessler, G. Kurz, J. G. Hacia, P. B. Dervan, H. Kessler
Structure Of A Stereoregular Phosphorothioate Dna/Rna Duplex
Nat. Struct. Biol. V. 5 271 1998
PubMed-ID: 9546216  |  Reference-DOI: 10.1038/NSB0498-271
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*DGP*(SC)P*(GS)P*(PST)P*(SC)P*(AS) P*(GS)P*(GS))-3')
    Chains: A
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - RNA (5'-R(*CP*CP*UP*GP*AP*CP*GP*C)-3')
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

NMR Structure (4, 7)
No.NameCountTypeFull Name
1AS1Mod. Residue2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE
2GS3Mod. ResidueGUANOSINE-5'-THIO-MONOPHOSPHATE
3PST1Mod. NucleotideTHYMIDINE-5'-THIOPHOSPHATE
4SC2Mod. Residue2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE

(-) Sites  (8, 8)

NMR Structure (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESC A:5 , GS A:7 , U B:11 , G B:12BINDING SITE FOR RESIDUE AS A 6
2AC2SOFTWARESC A:2 , C B:16BINDING SITE FOR RESIDUE DG A 1
3AC3SOFTWARESC A:2 , PST A:4 , A B:13 , C B:14 , G B:15BINDING SITE FOR RESIDUE GS A 3
4AC4SOFTWAREAS A:6 , GS A:8 , C B:10 , U B:11BINDING SITE FOR RESIDUE GS A 7
5AC5SOFTWAREGS A:7 , C B:9 , C B:10BINDING SITE FOR RESIDUE GS A 8
6AC6SOFTWAREGS A:3 , SC A:5 , A B:13BINDING SITE FOR RESIDUE PST A 4
7AC7SOFTWAREDG A:1 , GS A:3 , G B:15BINDING SITE FOR RESIDUE SC A 2
8AC8SOFTWAREPST A:4 , AS A:6 , G B:12 , A B:13BINDING SITE FOR RESIDUE SC A 5

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 8PSH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 8PSH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 8PSH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 8PSH)

(-) Exons   (0, 0)

(no "Exon" information available for 8PSH)

(-) 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:8
                                       
                  8psh A  1 Gcgtcagg  8
                             |||||||
                             |||||||
                             2-SC|||
                              3-GS||
                               4-PST
                                5-SC
                                 6-AS
                                  7-GS
                                   8-GS


Chain B from PDB  Type:RNA  Length:8
                                       
                  8psh B  9 CCUGACGC 16
   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 8PSH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 8PSH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 8PSH)

(-) Gene Ontology  (0, 0)

NMR Structure(hide GO term definitions)
    (no "Gene Ontology" information available for 8PSH)

 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
    AS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PST  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 8psh)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - model 1, sites PNG format | NMR Structure - all models 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
  8psh
    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 8PSH)

(-) Related Entries Specified in the PDB File

8drh MINIMIZED AVERAGE STRUCTURE