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 :  RIBOSOMAL PROTEIN S17: CHARACTERIZATION OF THE THREE-DIMENSIONAL STRUCTURE BY 1H-AND 15N-NMR
 
Authors :  B. L. Golden, D. W. Hoffman, V. Ramakrishnan, S. W. White
Date :  17 Aug 93  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (6x)
Keywords :  Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Golden, D. W. Hoffman, V. Ramakrishnan, S. W. White
Ribosomal Protein S17: Characterization Of The Three-Dimensional Structure By 1H And 15N Nmr.
Biochemistry V. 32 12812 1993
PubMed-ID: 8251502  |  Reference-DOI: 10.1021/BI00210A033
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOMAL PROTEIN S17
    Chains: A
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  
NMR Structure (6x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1RIP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_RS17_GEOSE_002 *S16GRS17_GEOSE  ---  ---AS15G
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIBOSOMAL_S17PS00056 Ribosomal protein S17 signature.RS17_GEOSE58-70  1A:57-69

(-) Exons   (0, 0)

(no "Exon" information available for 1RIP)

(-) 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:PROTEIN  Length:81
 aligned with RS17_GEOSE | P23828 from UniProtKB/Swiss-Prot  Length:87

    Alignment length:81
                                    15        25        35        45        55        65        75        85 
            RS17_GEOSE    6 QRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAVV 86
               SCOP domains d1ripa_ A: Ribosomal protein S17                                                  SCOP domains
               CATH domains 1ripA00 A:5-85 Nucleic acid-binding proteins                                      CATH domains
               Pfam domains ------Ribosomal_S17-1ripA01 A:11-79                                        ------ Pfam domains
         Sec.struct. author ...eeeeeeee.....eeeeeee..............eeeeeeee.......eeeeeeeee........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------G---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------RIBOSOMAL_S17---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  1rip A  5 QRKVYVGRVVSDKMDKTITVLVETYKKHPLYGKRVKYSKKYKAHDEHNEAKVGDIVKIMETRPLSATKRFRLVEIVEKAVR 85
                                    14        24        34        44        54        64        74        84
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: OB (224)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (RS17_GEOSE | P23828)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0019843    rRNA binding    Interacting selectively and non-covalently with ribosomal RNA.
    GO:0003735    structural constituent of ribosome    The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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

(-) 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 - 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
  1rip
    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 (structure derived) | HSSP (homology derived)
    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
  RS17_GEOSE | P23828
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  RS17_GEOSE | P23828
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RS17_GEOSE | P23828: 1eg0 1qd7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RIP)