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 :  CRYSTAL STRUCTURE OF N-TERMINALLY TRUNCATED PEROXIREDOXIN 4 FROM M. MUSCULUS
 
Authors :  K. Inaba, M. Suzuki
Date :  03 Sep 12  (Deposition) - 04 Sep 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peroxiredoxin Family, Thioredoxin Fold, Peroxiredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sato, R. Kojima, M. Okumura, M. Hagiwara, S. Masui, K. Maegawa, M. Saiki, T. Horibe, M. Suzuki, K. Inaba
Synergistic Cooperation Of Pdi Family Members In Peroxiredoxin 4-Driven Oxidative Protein Folding
Sci Rep V. 3 2456 2013
PubMed-ID: 23949117  |  Reference-DOI: 10.1038/SREP02456

(-) Compounds

Molecule 1 - PEROXIREDOXIN-4
    ChainsA, B
    EC Number1.11.1.15
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET15B
    FragmentUNP RESIDUES 87-274
    GenePRDX4
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymANTIOXIDANT ENZYME AOE372, PEROXIREDOXIN IV, PRX-IV, THIOREDOXIN PEROXIDASE AO372, THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE A0372

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2ACY1Ligand/IonACETIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:102 , LEU A:104 , ASP A:108 , HOH A:549 , ASP B:108 , HOH B:344 , HOH B:472BINDING SITE FOR RESIDUE 1PE A 301
2AC2SOFTWARELEU A:121 , HIS A:200 , HOH A:551BINDING SITE FOR RESIDUE ACY A 302

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:127 -B:248
2A:248 -B:127

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VWV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_2PS51352 Thioredoxin domain profile.PRDX4_MOUSE82-240
 
  2A:87-240
B:87-240

(-) Exons   (0, 0)

(no "Exon" information available for 3VWV)

(-) 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:182
 aligned with PRDX4_MOUSE | O08807 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:201
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 
          PRDX4_MOUSE    55 HFYAGGQVYPGEASRVSVADHSLHLSKAKISKPAPYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFKSINTEVVACSVDSQFTHLAWINTPRRQGGLGPIRIPLLSDLNHQISKDYGVYLEDSGHTLRGLFIIDDKGVLRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAGWKPG 255
               SCOP domains d3vwv         a_ A: a          utomated matches                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..---------.......----------......eeeeee..eeeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee..eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------THIOREDOXIN_2  PDB: A:87-240 UniProt: 82-240                                                                                                                   --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vwv A  74 HHSSG---------LVPRGSH----------MPAPYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFKSINTEVVACSVDSQFTHLAWINTPRRQGGLGPIRIPLLSDLNHQISKDYGVYLEDSGHTLRGLFIIDDKGVLRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAGWKPG 255
                                |    -    |   84|        - |      94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254 
                               78        79    85         86                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with PRDX4_MOUSE | O08807 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:183
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254   
          PRDX4_MOUSE    75 HSLHLSKAKISKPAPYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFKSINTEVVACSVDSQFTHLAWINTPRRQGGLGPIRIPLLSDLNHQISKDYGVYLEDSGHTLRGLFIIDDKGVLRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAGWKPGSE 257
               SCOP domains d3vwvb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..............eeeeee..eeeeee.hhhh..eeeeee.........hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.hhhhh........eee...hhhhhhh..ee....ee..eeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------THIOREDOXIN_2  PDB: B:87-240 UniProt: 82-240                                                                                                                   ----------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vwv B  75 HSSGLVPRGSHMPAPYWEGTAVINGEFKELKLTDYRGKYLVFFFYPLDFTFVCPTEIIAFGDRIEEFKSINTEVVACSVDSQFTHLAWINTPRRQGGLGPIRIPLLSDLNHQISKDYGVYLEDSGHTLRGLFIIDDKGVLRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAGWKPGSE 257
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254   

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VWV)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRDX4_MOUSE | O08807)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019471    4-hydroxyproline metabolic process    The chemical reactions and pathways involving 4-hydroxyproline, C5H9NO3, a derivative of the amino acid proline. The presence of hydroxyproline is essential to produce stable triple helical tropocollagen, hence the problems caused by ascorbate deficiency in scurvy. This unusual amino acid is also present in considerable amounts in the major glycoprotein of primary plant cell walls.
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0008584    male gonad development    The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure.
    GO:2000255    negative regulation of male germ cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation.
    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:0022417    protein maturation by protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure that results in the attainment of the full functional capacity of a protein.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.
    GO:0005790    smooth endoplasmic reticulum    The smooth endoplasmic reticulum (smooth ER or SER) has no ribosomes attached to it. The smooth ER is the recipient of the proteins synthesized in the rough ER. Those proteins to be exported are passed to the Golgi complex, the resident proteins are returned to the rough ER and the lysosomal proteins after phosphorylation of their mannose residues are passed to the lysosomes. Glycosylation of the glycoproteins also continues. The smooth ER is the site of synthesis of lipids, including the phospholipids. The membranes of the smooth ER also contain enzymes that catalyze a series of reactions to detoxify both lipid-soluble drugs and harmful products of metabolism. Large quantities of certain compounds such as phenobarbital cause an increase in the amount of the smooth ER.

 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vwv)
 

(-) 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
  3vwv
    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
  PRDX4_MOUSE | O08807
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.11.1.15
    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
  PRDX4_MOUSE | O08807
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PRDX4_MOUSE | O088073vwu 3w8j 3wgx

(-) Related Entries Specified in the PDB File

2pn8 CRYSTAL STRUCTURE OF N-TERMINALLY TRUNCATED PRX4 FROM H. SAPIENCE
3vwu
3vww
3w8j