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
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A DUF151 FAMILY PROTEIN (TM0160) FROM THERMOTOGA MARITIMA AT 2.8 A RESOLUTION
 
Authors :  G. Spraggon, D. Panatazatos, H. E. Klock, I. A. Wilson, V. L. Woods Jr. , S. A. Lesley, Joint Center For Structural Genomics (Jcsg)
Date :  02 Mar 04  (Deposition) - 01 Mar 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Spraggon, D. Pantazatos, H. E. Klock, I. A. Wilson, V. L. Woods Jr. , S. A. Lesley
On The Use Of Dxms To Produce More Crystallizable Proteins: Structures Of The T. Maritima Proteins Tm0160 And Tm1171.
Protein Sci. V. 13 3187 2004
PubMed-ID: 15557262  |  Reference-DOI: 10.1110/PS.04939904

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN TM0160
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0160
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1SJ5)

(-) Sites  (0, 0)

(no "Site" information available for 1SJ5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SJ5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SJ5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1SJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 1SJ5)

(-) 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:143
 aligned with Q9WY07_THEMA | Q9WY07 from UniProtKB/TrEMBL  Length:181

    Alignment length:171
                             1                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169 
         Q9WY07_THEMA     - -MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGACEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLTYTDEEDEEAALIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNETQDEEEEFKKFVENLNIDTFKQMIE 170
               SCOP domains d1sj5a_ A: Hypothetical protein TM0160                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee......eeeeeee....eeeeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeee...--------..eeeeeehhhhhhhhhhhhh..eeeehhhhhhhhee.hhhh--------------------hhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sj5 A   0 HMRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLT--------AALIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIELEVNE--------------------RDLIN 150
                                     9        19        29        39        49        59        69        79        89     |   -    |  109       119       129       139     |   -         -      |149 
                                                                                                                          95      104                                      145                  146    


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with Q9WY07_THEMA | Q9WY07 from UniProtKB/TrEMBL  Length:181

    Alignment length:142
                             1                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139  
         Q9WY07_THEMA     - -MRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGACEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLTYTDEEDEEAALIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIEL 141
               SCOP domains d1sj5b_ B: Hypothetical protein TM0160                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----DNase-RNase-1sj5B01 B:4-141                                                                                                                Pfam domains (1)
           Pfam domains (2) ----DNase-RNase-1sj5B02 B:4-141                                                                                                                Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeee....eeeeeeee......eeee.hhhhhhhhhhhhh.......hhhhhhhhhhhhh.eeeeeeeeeee....eeeeeeeee...-----....eeeeeehhhhhhhhhhhhh..eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sj5 B   0 HMRKAWVKTLALDRVSNTPVVILGIEGTNRVLPIWIGAAEGHALALAMEKMEFPRPLTHDLLLSVLESLEARVDKVIIHSLKDNTFYATLVIRDLTY-----EEAALIDIDSRPSDAIILAVKTGAPIFVSDNLVEKHSIEL 141
                                     9        19        29        39        49        59        69        79        89      |  -  |    109       119       129       139  
                                                                                                                           96   102
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1SJ5)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DNase-RNase] (2)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9WY07_THEMA | Q9WY07)
molecular function
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

 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
(no "Ligands, Modified Residues, Ions" information available for 1sj5)
 
  Sites
(no "Sites" information available for 1sj5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1sj5)
 

(-) 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 ](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
  1sj5
    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
  Q9WY07_THEMA | Q9WY07
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q9WY07_THEMA | Q9WY07
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9WY07_THEMA | Q9WY07: 1vjl

(-) Related Entries Specified in the PDB File

1o5y NATIVE TM0160