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(-) Description

Authors :  V. Ramakrishnan, S. W. White
Date :  30 Aug 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  V. Ramakrishnan, S. W. White
The Structure Of Ribosomal Protein S5 Reveals Sites Of Interaction With 16S Rrna.
Nature V. 358 768 1992
PubMed-ID: 1508272  |  Reference-DOI: 10.1038/358768A0
(for further references see the PDB file header)

(-) Compounds

    Organism Taxid1422

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1SPRAUTHORARG A:20 , VAL A:21 , ALA A:22 , LYS A:23 , VAL A:24 , VAL A:25 , LYS A:26 , GLY A:27 , GLY A:28 , ARG A:29 , ARG A:30 , LEU A:31 , ARG A:32PROPOSED SITES FOR INTERACTION WITH 16S R-RNA

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
1S5_DSRBDPS50881 S5 double stranded RNA-binding domain profile.RS5_GEOSE11-74  1A:11-74
2RIBOSOMAL_S5PS00585 Ribosomal protein S5 signature.RS5_GEOSE28-60  1A:28-60
Biological Unit 1 (2, 4)
1S5_DSRBDPS50881 S5 double stranded RNA-binding domain profile.RS5_GEOSE11-74  2A:11-74
2RIBOSOMAL_S5PS00585 Ribosomal protein S5 signature.RS5_GEOSE28-60  2A:28-60

(-) Exons   (0, 0)

(no "Exon" information available for 1PKP)

(-) Sequences/Alignments

Asymmetric 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:PROTEIN  Length:145
 aligned with RS5_GEOSE | P02357 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
               SCOP domains d1pkpa2 A:4-77 Ribosomal S5 protein, N-terminal domain                    d1pkpa1 A:78-148 Ribosomal protein S5, C-terminal domain                SCOP domains
               CATH domains 1pkpA01 A:4-73  [code=, no name defined]                   1pkpA02 A:74-148  [code=, no name defined]                       CATH domains
               Pfam domains ------Ribosomal_S5-1pkpA01 A:10-76                                       --------Ribosomal_S5_C-1pkpA02 A:85-148                                  Pfam domains
         Sec.struct. author ......eeeeeeeeeee...........eeeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh.............eeeeeee..eeeeeee..........hhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------S5_DSRBD  PDB: A:11-74 UniProt: 11-74                           -------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------RIBOSOMAL_S5  PDB: A:28-60       ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
Clan: DSRM (45)
Clan: S5 (103)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (RS5_GEOSE | P02357)
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:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    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: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.
    GO:0015935    small ribosomal subunit    The smaller of the two subunits of a ribosome.


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 Related Entries

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

        RS5_GEOSE | P023571dv4 1eg0 1qd7

(-) Related Entries Specified in the PDB File

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