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 THIOREDOXIN DOMAIN OF HUMAN THIOREDOXIN-LIKE PROTEIN 2
 
Authors :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 06  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pkc-Interacting Cousin Of Thioredoxin, Pkc-Theta- Interacting Protein, Picot, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
The Solution Structure Of The Thioredoxin Domain Of Human Thioredoxin-Like Protein 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN-LIKE PROTEIN 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP050302-06
    Expression System Vector TypePLASMID
    FragmentTHIOREDOXIN DOMAIN, RESIDUES 8-124
    GeneTXNL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymPKC-INTERACTING COUSIN OF THIOREDOXIN, PKC-THETA- INTERACTING PROTEIN, PKCQ-INTERACTING PROTEIN

 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 2DIY)

(-) Sites  (0, 0)

(no "Site" information available for 2DIY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DIY)

(-) 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, 20Val A:92 -Pro A:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016875Q21HGLRX3_HUMANPolymorphism13991AQ28H
2UniProtVAR_016876P123SGLRX3_HUMANPolymorphism2274217AP127S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.GLRX3_HUMAN1-117  1A:8-124

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003686441ENSE00002174390chr10:131934663-131934776114GLRX3_HUMAN1-31311A:8-3831
1.2ENST000003686442ENSE00000728668chr10:131943475-131943583109GLRX3_HUMAN31-67371A:38-7437
1.4ENST000003686444ENSE00000728671chr10:131958259-13195833375GLRX3_HUMAN68-92251A:75-9925
1.5bENST000003686445bENSE00000728676chr10:131959060-131959261202GLRX3_HUMAN93-160681A:100-130 (gaps)34
1.6ENST000003686446ENSE00000728678chr10:131964771-131964943173GLRX3_HUMAN160-217580--
1.7ENST000003686447ENSE00000728681chr10:131965183-13196524462GLRX3_HUMAN218-238210--
1.8ENST000003686448ENSE00000728683chr10:131967697-13196775458GLRX3_HUMAN238-257200--
1.9ENST000003686449ENSE00000728687chr10:131969848-13196990053GLRX3_HUMAN258-275180--
1.10ENST0000036864410ENSE00000728691chr10:131973131-13197317040GLRX3_HUMAN275-288140--
1.11ENST0000036864411ENSE00000577957chr10:131973261-13197335393GLRX3_HUMAN289-319310--
1.12aENST0000036864412aENSE00001217321chr10:131977606-13197768479GLRX3_HUMAN320-335160--
1.13bENST0000036864413bENSE00001217252chr10:131978377-131978640264GLRX3_HUMAN-00--

(-) 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:130
 aligned with GLRX3_HUMAN | O76003 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:133
                                   1                                                                                                                             
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123   
          GLRX3_HUMAN     - -------MAAGAAEAAVAAVEEVGSAGQFEELLRLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSGSFLPSAN 126
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eee.hhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhh.....eeeee....eeeeee..hhhhhhhhhhhhhh..---.... Sec.struct. author
                 SAPs(SNPs) ---------------------------H-----------------------------------------------------------------------------------------------------S--- SAPs(SNPs)
                    PROSITE -------THIOREDOXIN_2  PDB: A:8-124 UniProt: 1-117                                                                           --------- PROSITE
           Transcript 1 (1) -------Exon 1.1  PDB: A:8-38          ------------------------------------Exon 1.4  PDB: A:75-99   Exon 1.5b  PDB: A:100-130 (gaps)   Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.2  PDB: A:38-74 UniProt: 31-67----------------------------------------------------------- Transcript 1 (2)
                 2diy A   1 GSSGSSGMAAGAAEAAVAAVEEVGSAGQFEELLRLKAKSLLVVHFWAPWAPQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSVPTFLFFKNSQKIDRLDGAHAPELTKKVQRHASSG---PSSG 130
                                    10        20        30        40        50        60        70        80        90       100       110       120     | 127   
                                                                                                                                                       126 127   

   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 2DIY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DIY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (GLRX3_HUMAN | O76003)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0010614    negative regulation of cardiac muscle hypertrophy    Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0002026    regulation of the force of heart contraction    Any process that modulates the extent of heart contraction, changing the force with which blood is propelled.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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 2diy)
 
  Sites
(no "Sites" information available for 2diy)
 
  Cis Peptide Bonds
    Val A:92 - Pro A:93   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2diy
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GLRX3_HUMAN | O76003
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GLRX3_HUMAN | O76003
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GLRX3_HUMAN | O760032wz9 2yan 3zyw

(-) Related Entries Specified in the PDB File

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