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 HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMOMYCIN
 
Authors :  J. Kondo, M. Hainrichson, I. Nudelman, D. Shallom-Shezifi, T. Baasov, E. Westhof
Date :  02 Dec 06  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoglycoside, Antibiotics, Ribosome, Decoding Site, Homo Sapiens, Eukaryote, Cytoplasmic, Translation Inhibition, Stop Codon Readthrough, Unspecific Binding, Rna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kondo, M. Hainrichson, I. Nudelman, D. Shallom-Shezifi, C. M. Barbieri, D. S. Pilch, E. Westhof, T. Baasov
Differential Selectivity Of Natural And Synthetic Aminoglycosides Towards The Eukaryotic And Prokaryotic Decoding A Sites.
Chembiochem V. 8 1700 2007
PubMed-ID: 17705310  |  Reference-DOI: 10.1002/CBIC.200700271
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP *UP*CP*GP*C)-3')
    Chains: A, B
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 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
1PAR1Ligand/IonPAROMOMYCIN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREG A:8 , C A:9 , U B:33 , C B:34 , G B:36 , G B:37 , A B:38 , A B:39BINDING SITE FOR RESIDUE PAR B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O3W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O3W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O3W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O3W)

(-) Exons   (0, 0)

(no "Exon" information available for 2O3W)

(-) 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:22
                                                     
                  2o3w A  2 UGCGUCGCUCCGGAAAAGUCGC 23
                                    11        21  


Chain B from PDB  Type:RNA  Length:21
                                                    
                  2o3w B 26 GCGUCGCUCCGGAAAAGUCGC 46
                                    35        45
   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 2O3W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O3W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O3W)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2O3W)

 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
    PAR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2o3w)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  2o3w
    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 2O3W)

(-) Related Entries Specified in the PDB File

2fqn HOMO SAPIENS CYTOPLASMIC A SITE WITHOUT ANY AMINOGLYCOSIDES (CYTO-FREE)
2g5k HOMO SAPIENS CYTOPLASMIC A SITE COMPLEXED WITH APRAMYCIN (CYTO/APRAMYCIN)
2o3v CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB33
2o3x CRYSTAL STRUCTURE OF THE PROKARYOTIC RIBOSOMAL DECODING SITE COMPLEXED WITH PAROMAMINE DERIVATIVE NB30
2o3y CRYSTAL STRUCTURE OF THE HOMO SAPIENS CYTOPLASMIC RIBOSOMAL DECODING SITE IN PRESENCE OF PAROMAMINE DERIVATIVE NB30