Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  THE SOLUTION STRUCTURE OF THE THIRD THIOREDOXIN DOMAIN OF HUMAN THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 30 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Thioredoxin-Like Protein P46, Endoplasmic Reticulum Protein Erp46, Tlp46, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Third Thioredoxin Domain Of Human Thioredoxin Domain-Containing Protein 5
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN DOMAIN-CONTAINING PROTEIN 5
    Chains: A
    Engineered: YES
    Expression System: CELL FREE SYNTHESIS
    Expression System Plasmid: P050302-28
    Expression System Vector Type: PLASMID
    Fragment: 3RD THIOREDOXIN DOMAIN
    Gene: TXNDC5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: THIOREDOXIN-LIKE PROTEIN P46, ENDOPLASMIC RETICULUM PROTEIN ERP46

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DIZ)

(-) Sites  (0, 0)

(no "Site" information available for 2DIZ)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:66 -A:73

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:81 -Pro A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DIZ)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.TXND5_HUMAN36-169
170-295
304-429		  1-
-
A:7-114
2THIOREDOXIN_1PS00194 Thioredoxin family active site.TXND5_HUMAN81-99
209-227
342-360		  1-
-
A:27-45
3ER_TARGETPS00014 Endoplasmic reticulum targeting sequence.TXND5_HUMAN429-432  1A:114-117

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003797571ENSE00001482400chr6:7911047-7910747301TXND5_HUMAN1-88880--
1.3ENST000003797573ENSE00002035816chr6:7904956-7904807150TXND5_HUMAN88-138510--
1.4bENST000003797574bENSE00002030712chr6:7899914-7899809106TXND5_HUMAN138-173360--
1.5bENST000003797575bENSE00002020031chr6:7895435-789533997TXND5_HUMAN174-206330--
1.6ENST000003797576ENSE00002062288chr6:7891969-7891854116TXND5_HUMAN206-244390--
1.7ENST000003797577ENSE00002051337chr6:7889814-788972887TXND5_HUMAN245-273290--
1.8cENST000003797578cENSE00002072823chr6:7889081-7888938144TXND5_HUMAN274-321481A:1-66
1.9ENST000003797579ENSE00002061487chr6:7886276-788619483TXND5_HUMAN322-349281A:7-3428
1.10ENST0000037975710ENSE00002026226chr6:7884721-7884592130TXND5_HUMAN349-392441A:34-7744
1.11cENST0000037975711cENSE00001964269chr6:7883499-78817501750TXND5_HUMAN393-432401A:78-11740

(-) Sequences/Alignments

NMR Structure
   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:117
 aligned with TXND5_HUMAN | Q8NBS9 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:133
                                   309       319       329       339       349       359       369       379       389       399       409       419       429   
          TXND5_HUMAN   300 GATETVTPSEAPVLAAEPEADKGTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQAKDEL 432
               SCOP domains d2diza                _ A: automated matches                                                                                          SCOP domains
               CATH domains 2dizA0                0 A:1-117 Glutaredoxin                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----------------...ee.....hhhhhhh..eeeeee....hhhhhhhhhhhhhhhh........eeeeee...hhhhhhhh......eee...............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----THIOREDOXIN_2  PDB: A:7-114 UniProt: 304-429                                                                                  --- PROSITE (1)
                PROSITE (2) ------------------------------------------THIOREDOXIN_1      --------------------------------------------------------------------ER_T PROSITE (2)
           Transcript 1 (1) Exon 1.8c  PDB: A:1-6 ---------------------------Exon 1.10  PDB: A:34-77 UniProt: 349-392    Exon 1.11c  PDB: A:78-117                Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.9  PDB: A:7-34       ----------------------------------------------------------------------------------- Transcript 1 (2)
                 2diz A   1 GSSGSS----------------GTVLALTENNFDDTIAEGITFIKFYAPWCGHCKTLAPTWEELSKKEFPGLAGVKIAEVDCTAERNICSKYSVRGYPTLLLFRGGKKVSEHSGGRDLDSLHRFVLSQAKDEL 117
                                 |   -         -  |     14        24        34        44        54        64        74        84        94       104       114   
                                 6                7
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DIZ)

(-) Gene Ontology  (12, 12)

NMR Structure(hide GO term definitions)
Chain A   (TXND5_HUMAN | Q8NBS9)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003756    protein disulfide isomerase activity    Catalysis of the rearrangement of both intrachain and interchain disulfide bonds in proteins.
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0034976    response to endoplasmic reticulum stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.

 Visualization

(-) Interactive Views

NMR Structure
  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 2diz)
 
  Sites
(no "Sites" information available for 2diz)
 
  Cis Peptide Bonds
    Tyr A:81 - Pro A:82   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2diz
    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
  TXND5_HUMAN | Q8NBS9
    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)
  (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
  TXND5_HUMAN | Q8NBS9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TXND5_HUMAN | Q8NBS9: 3uj1 3uvt 3wgd 3wge 3wgx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DIZ)