Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL GENOMICS OF CAENORHABDITIS ELEGANS: STRUCTURE OF A PROTEIN WITH UNKNOWN FUNCTION
 
Authors :  J. Symersky, S. Li, R. Bunzel, N. Schormann, D. Luo, W. Y. Huang, S. Qiu, R. Gray, Y. Zhang, A. Arabashi, S. Lu, C. H. Luan, J. Tsao, L. Delucas, M. Luo, Southeast Collaboratory For Structural Genomics (Secsg)
Date :  16 May 04  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Symersky, S. Li, R. Bunzel, N. Schormann, D. Luo, W. Y. Huang, S. Qiu, R. Gray, Y. Zhang, A. Arabashi, S. Lu, C. H. Luan, J. Tsao, L. Delucas, M. Luo
Structural Genomics Of Caenorhabditis Elegans: Structure Of A Protein With Unknown Function.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN 1D10
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15G
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-206
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239

 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
1MLI1Ligand/IonMALONATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:139 , ASN A:141 , LYS A:152 , HOH A:315BINDING SITE FOR RESIDUE MLI A 207

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:82
2A:90 -A:140

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:171 -Pro A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T9F)

(-) Exons   (0, 0)

(no "Exon" information available for 1T9F)

(-) 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:178
 aligned with O61793_CAEEL | O61793 from UniProtKB/TrEMBL  Length:206

    Alignment length:178
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189        
         O61793_CAEEL    20 YADEDFVTCYSVLKFINANDGSRLHSHDVKYGSGSGQQSVTAVKNSDDINSHWQIFPALNAKCNRGDAIKCGDKIRLKHLTTGTFLHSHHFTAPLSKQHQEVSAFGSEAESDTGDDWTVICNGDEWLESEQFKLRHAVTGSYLSLSGQQFGRPIHGQREVVGTDSITGGSAWKVAEGI 197
               SCOP domains d1t9fa_ A: Hypothetical protein R12E2.13 (1D10)                                                                                                                                    SCOP domains
               CATH domains 1t9fA00 A:-1-197  [code=2.80.10.50, no name defined]                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.....eeeeeeee.......eeeeee....hhhh.eeeee................eeeeee.....eeeeeeee.......eeeeee......hhhh.eeee..........eeeeee.....eeeeeeee........eeeeee........eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t9f A  -1 GSDEDFVTCYSVLKFINANDGSRLHSHDVKYGSGSGQQSVTAVKNSDDINSHWQIFPALNAKCNRGDAIKCGDKIRLKHLTTGTFLHSHHFTAPLSKQHQEVSAFGSEAESDTGDDWTVICNGDEWLESEQFKLRHAVTGSYLSLSGQQFGRPIHGQREVVGTDSITGGSAWKVAEGI 197
                             ||     29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189        
                             0|                                                                                                                                                                               
                             22
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1T9F)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O61793_CAEEL | O61793)
molecular function
    GO:0004169    dolichyl-phosphate-mannose-protein mannosyltransferase activity    Catalysis of the reaction: dolichyl phosphate D-mannose + protein = dolichyl phosphate + O-D-mannosylprotein.
biological process
    GO:0000032    cell wall mannoprotein biosynthetic process    The chemical reactions and pathways resulting in the formation of cell wall mannoproteins, any cell wall protein that contains covalently bound mannose residues.
    GO:0044845    chain elongation of O-linked mannose residue    Extension of the O-linked mannose residue of a mannoprotein by the stepwise addition of further mannose molecules.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0035269    protein O-linked mannosylation    The transfer of mannose from dolichyl activated mannose to the hydroxyl group of a seryl or threonyl residue of a protein acceptor molecule, to form an O-linked protein-sugar linkage.
    GO:1900101    regulation of endoplasmic reticulum unfolded protein response    Any process that modulates the frequency, rate or extent of endoplasmic reticulum unfolded protein response.
cellular component
    GO:0031502    dolichyl-phosphate-mannose-protein mannosyltransferase complex    A complex that possesses dolichyl-phosphate-mannose-protein mannosyltransferase activity; usually includes members of the PMT1 and PMT2 protein subfamilies.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 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
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:171 - Pro A:172   [ RasMol ]  
 

(-) 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 | Asym./Biol. Unit - sites 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
  1t9f
    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
  O61793_CAEEL | O61793
    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
  O61793_CAEEL | O61793
    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 1T9F)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1T9F)