Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TWO ARCHAEAL PELOTAS REVEAL INTER-DOMAIN STRUCTURAL PLASTICITY
 
Authors :  H. H. Lee, J. Y. Jang, H. -J. Yoon, S. J. Kim, S. W. Suh
Date :  09 Aug 10  (Deposition) - 01 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Sm Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. H. Lee, J. Y. Jang, H. -J. Yoon, S. J. Kim, S. W. Suh
Crystal Structures Of Two Archaeal Pelotas Reveal Inter-Domain Structural Plasticity
Biochem. Biophys. Res. Commun. V. 399 600 2010
PubMed-ID: 20682285  |  Reference-DOI: 10.1016/J.BBRC.2010.07.121

(-) Compounds

Molecule 1 - PROTEIN PELOTA HOMOLOG
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28B(+)
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287

 Structural Features

(-) Chains, Units

  1
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 3OBW)

(-) Sites  (0, 0)

(no "Site" information available for 3OBW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:262 -Pro A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OBW)

(-) 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:321
 aligned with PELO_SULSO | P96026 from UniProtKB/Swiss-Prot  Length:344

    Alignment length:338
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
           PELO_SULSO     7 DEKRQAVKLHIESEDDLWLLHLILEKDDKVVAKTTRDVGLGKESRRIPMTIILKVDYTEFQEFTNRLRIHGIIEDAPERFGIKGAHHTINLDIGDEIIIIKQQWNKYVLDRLKRQANKRSRIIIALVDFDEYLIAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIATELAEYVKQYDPDAILLAGPGFFKEEVSKKVNAILKNKKIYIDSVSSATRAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLLSSDEQERLTIERMLEDIENKRGEVILVPKESPIYFELKNLTGILAILRFRIN 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains eRF1_1-3obwA03 A:7-110                                                                                                --eRF1_2-3obwA02 A:127-242                                                                                            --eRF1_3-3obwA01 A:245-343                                                                           - Pfam domains
         Sec.struct. author ......eeee..hhhhhhhhhhhh....eeeeeeeee..---...eeeeeeeeeeeeeeee....eeeeeeeeee.hhhhh....eeeeee....eeeee....--------------...eeeeeee..eeeeeee....ee...eee.hhhh...hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh.....eeeee.....hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeehhhhhhhhhhhh.eeeeeee.hhhh.hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhh..eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3obw A   7 DEKRQAVKLHIESEDDLWLLHLILEKDDKVVAKTTRDVG---ESRRIPMTIILKVDYTEFQEFTNRLRIHGIIEDAPERFGIKGAHHTINLDIGDEIIIIKQQW--------------RSRIIIALVDFDEYLIAIPFEQGIKILSEKSLRPLNEEEGIIEQNALEIATELAEYVKQYDPDAILLAGPGFFKEEVSKKVNAILKNKKIYIDSVSSATRAGLHEVLKRDIIDKIMTDYEIAIGAKKMEKAMELLAKQPELVTYGLEQVKNAIEMGAVETVLVIEDLLSSDEQERLTIERMLEDIENKRGEVILVPKESPIYFELKNLTGILAILRFRIN 344
                                    16        26        36        |-  |     56        66        76        86        96       106   |     -       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336        
                                                                 45  49                                                          110            125
   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 3OBW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: RNA_ribose_bind (78)
(-)
Clan: S11_L18p (67)
(-)
Clan: no clan defined [family: eRF1_1] (6)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (PELO_SULSO | P96026)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0071025    RNA surveillance    The set of processes involved in identifying and degrading defective or aberrant RNAs.
    GO:0070966    nuclear-transcribed mRNA catabolic process, no-go decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA with stalls in translation elongation.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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 3obw)
 
  Sites
(no "Sites" information available for 3obw)
 
  Cis Peptide Bonds
    Gln A:262 - Pro A:263   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  3obw
    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
  PELO_SULSO | P96026
    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)
  3.1.-.-
    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
  PELO_SULSO | P96026
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3OBW)

(-) Related Entries Specified in the PDB File

3oby AF PELOTA