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
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING
 
Authors :  C. Ban, B. Ramakrishnan, M. Sundaralingam
Date :  05 Dec 94  (Deposition) - 31 Mar 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  A-Dna/Rna, Double Helix, Dna-Rna Hybrid (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ban, B. Ramakrishnan, M. Sundaralingam
Crystal Structure Of The Highly Distorted Chimeric Decamer R(C)D(Cggcgccg)R(G). Spermine Complex--Spermine Binding To Phosphate Only And Minor Groove Tertiary Base-Pairing.
Nucleic Acids Res. V. 22 5466 1994
PubMed-ID: 7816639  |  Reference-DOI: 10.1093/NAR/22.24.5466
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA/RNA (5'-R(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)- R(*G)-3')
    ChainsA, B
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SPM1Ligand/IonSPERMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC A:5 , DG A:6 , DG A:9 , HOH A:29 , HOH A:46 , HOH A:56 , HOH A:87 , DG B:13 , DG B:14 , DG B:19 , G B:20 , HOH B:33 , HOH B:52BINDING SITE FOR RESIDUE SPM A 21

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 100D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 100D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 100D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 100D)

(-) Exons   (0, 0)

(no "Exon" information available for 100D)

(-) 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
                                         
                  100d A  1 CCGGCGCCGG 10
                                    10

Chain B from PDB  Type:DNA/RNA  Length:10
                                         
                  100d B 11 CCGGCGCCGG 20
                                    20

   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 100D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 100D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 100D)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 100D)

 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
    SPM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 100d)
 

(-) 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
Insightii
  ribbon, sticks: ribonucleotides: ball and sticks; spermine
  ribbon, sticks: ribonucleotides: ball and sticks; spermine; water
  spacefill, water
Setor
  sticks, spermine
  spacefill, spermine
  ribbon, sticks, labeling, spermine
Distance Plot
  representative atom O3*

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  100d
    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 100D)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 100D)