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(-) Description

Title :  GDP-BOUND STRUCTUE OF TM YLQF
 
Authors :  D. J. Kim, J. Y. Jang, H. -J. Yoon, S. W. Suh
Date :  26 Mar 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Ylqf, Circular Permutation, Gdp, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Kim, J. Y. Jang, H. -J. Yoon, S. W. Suh
Crystal Structure Of Ylqf, A Circularly Permuted Gtpase: Implications For Its Gtpase Activation In 50 S Ribosomal Subunit Assembly
Proteins V. 72 1363 2008
PubMed-ID: 18536017  |  Reference-DOI: 10.1002/PROT.22112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTM0768
    Organism ScientificTHERMOTOGA MARITIMA
    Organism Taxid2336
    SynonymYLQF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , LYS A:55 , ASP A:57 , ILE A:58 , LYS A:73 , HIS A:82 , LYS A:83 , ASN A:109 , THR A:110 , GLY A:111 , LYS A:112 , SER A:113 , THR A:114 , HOH A:540 , HOH A:561 , HOH A:582 , HOH A:583 , HOH A:594 , HOH A:604BINDING SITE FOR RESIDUE GDP A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CNO)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Arg A:13 -Gln A:14
2Lys A:120 -Gly A:121
3Gly A:121 -Lys A:122
4Glu A:249 -Asp A:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CNO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CNO)

(-) Exons   (0, 0)

(no "Exon" information available for 3CNO)

(-) 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:PROTEIN  Length:227
 aligned with RBGA_THEMA | Q9WZM6 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:238
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242        
           RBGA_THEMA    13 RQIKDLLRLVNTVVEVRDARAPFATSAYGVDFSRKETIILLNKVDIADEKTTKKWVEFFKKQGKRVITTHKGEPRKVLLKKLSFDRLARVLIVGVPNTGKSTIINKLKGKRASSVGAQPGITKGIQWFSLENGVKILDTPGILYKNIFSEDLAAKLLLVGSLPVERIEDQRIFERAFEIFARSIGIESSFSEFFEDFARKRGLLKKGGVPDIERALMLFFTEVAQGKAGRVSFERPED 250
               SCOP domains d3cnoa_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eeeeeee.................eeeeeeehhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhh.....eeeeee....hhhhhhhhhhh...-----------...eee.....eee...ee......hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..ee...eehhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cno A  13 RQIKDLLRLVNTVVEVRDARAPFATSAYGVDFSRKETIILLNKVDIADEKTTKKWVEFFKKQGKRVITTHKGEPRKVLLKKLSFDRLARVLIVGVPNTGKSTIINKLKGKRA-----------GIQWFSLENGVKILDTPGILYKNIFSEDLAAKLLLVGSLPVERIEDQRIFERAFEIFARSIGIESSFSEFFEDFARKRGLLKKGGVPDIERALMLFFTEVAQGKAGRVSFERPED 250
                                    22        32        42        52        62        72        82        92       102       112       122 |       -   |   142       152       162       172       182       192       202       212       222       232       242        
                                                                                                                                         124         136                                                                                                                  

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  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)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CNO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CNO)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RBGA_THEMA | Q9WZM6)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RBGA_THEMA | Q9WZM63cnl 3cnn

(-) Related Entries Specified in the PDB File

3cnl 3cnn