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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E.COLI 23S RRNA AT 1.04 RESOLUTION
 
Authors :  C. C. Correll, J. Beneken, M. J. Plantinga, M. Lubbers, Y. L. Chan
Date :  22 Aug 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.04
Chains :  Asym./Biol. Unit :  A
Keywords :  Sarcin/Ricin Domain, Ribonucleic Acid, Rna Recognition, High Resolution, Ribosomes (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Correll, J. Beneken, M. J. Plantinga, M. Lubbers, Y. L. Chan
The Common And Distinctive Features Of The Bulged-G Motif Based On A 1. 04 A Resolution Rna Structure
Nucleic Acids Res. V. 31 6806 2003
PubMed-ID: 14627814  |  Reference-DOI: 10.1093/NAR/GKG908
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SARCIN/RICIN 23S RRNA
    ChainsA
    EngineeredYES
    FragmentSARCIN/RICIN DOMAIN
    Other DetailsTHE 23S RIBOSOMAL RNA WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE 23S RIBOSOMAL RNA IS NATURALLY FOUND IN ESCHERICHIA COLI (BACTERIA).
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1Q9A)

(-) Sites  (0, 0)

(no "Site" information available for 1Q9A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q9A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q9A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q9A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q9A)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q9A)

(-) 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:RNA  Length:27
                                                            
                1q9a A 2647 UGCUCCUAGUACGAGAGGACCGGAGUG 2673
                                  2656      2666       

   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 1Q9A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Q9A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q9A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Q9A)

 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
(no "Ligands, Modified Residues, Ions" information available for 1q9a)
 
  Sites
(no "Sites" information available for 1q9a)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1q9a)
 

(-) 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
  1q9a
    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 1Q9A)

(-) Related Entries Specified in the PDB File

1jbr CRYSTAL STRUCTURE OF THE RIBOTOXIN RESTRICTOCIN AND A 31- MER SRD RNA INHIBITOR
1jbs CRYSTAL STRUCTURE OF RIBOTOXIN RESTRICTOCIN AND A 29-MER SRD RNA ANALOG
1msy GUAA TETRALOOP MUTANT OF SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA
1q93 CRYSTAL STRUCTURE OF A MUTANT OF THE SARCIN/RICIN DOMAIN FROM RAT 28S RRNA
1q96 CRYSTAL STRUCTURE OF A MUTANT OF THE SARCIN/RICIN DOMAIN FROM RAT 28S RRNA
480d CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA
483d CRYSTAL STRUCTURE OF THE SARCIN/RICIN DOMAIN FROM E. COLI 23 S RRNA