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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE POPLAR GLUTATHIONE PEROXIDASE 5 IN THE OXIDIZED FORM
 
Authors :  C. S. Koh, C. Didierjean, N. Navrot, S. Panjikar, G. Mulliert, N. Rouhier, J. -P. Jacquot, A. Aubry, O. Shawkataly, C. Corbier
Date :  16 Mar 07  (Deposition) - 24 Jul 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thioredoxin Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Koh, C. Didierjean, N. Navrot, S. Panjikar, G. Mulliert, N. Rouhier, J. P. Jacquot, A. Aubry, O. Shawkataly, C. Corbier
Crystal Structures Of A Poplar Thioredoxin Peroxidase That Exhibits The Structure Of Glutathione Peroxidases: Insights Into Redox-Driven Conformational Changes.
J. Mol. Biol. V. 370 512 2007
PubMed-ID: 17531267  |  Reference-DOI: 10.1016/J.JMB.2007.04.031
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTATHIONE PEROXIDASE 5
    Chains: A, B
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3D
    Expression System Strain: BL21 (DE3) PSBET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PTGPX5
    Organism Scientific: POPULUS TRICHOCARPA X POPULUS DELTOIDES
    Organism Taxid: 3695

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION

(-) Sites  (0, 0)

(no "Site" information available for 2P5R)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:92
2B:44 -B:92

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P5R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P5R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P5R)

(-) Exons   (0, 0)

(no "Exon" information available for 2P5R)

(-) 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:164
 aligned with A3FNZ8_9ROSI | A3FNZ8 from UniProtKB/TrEMBL  Length:170

    Alignment length:164
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    
         A3FNZ8_9ROSI     6 SKNPESVHDFTVKDAKENDVDLSIFKGKVLLIVNVASKCGMTNSNYAEMNQLYEKYKDQGLEILAFPCNQFGEEEPGTNDQITDFVCTRFKSEFPIFDKIDVNGENASPLYRFLKLGKWGIFGDDIQWNFAKFLVNKDGQVVDRYYPTTSPLSLERDIKQLLEI 169
               SCOP domains d2p5ra_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhh.eee.....eee.hhhh..eeeeeeee......hhhhhhhhhhhhhhh...eeeeeeee.......................................hhhhhhhh................eeee.....eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p5r A   6 SKNPESVHDFTVKDAKENDVDLSIFKGKVLLIVNVASKCGMTNSNYAEMNQLYEKYKDQGLEILAFPCNQFGEEEPGTNDQITDFVCTRFKSEFPIFDKIDVNGENASPLYRFLKLGKWGIFGDDIQWNFAKFLVNKDGQVVDRYYPTTSPLSLERDIKQLLEI 169
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    


Chain B from PDB  Type:PROTEIN  Length:164
 aligned with A3FNZ8_9ROSI | A3FNZ8 from UniProtKB/TrEMBL  Length:170

    Alignment length:164
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165    
         A3FNZ8_9ROSI     6 SKNPESVHDFTVKDAKENDVDLSIFKGKVLLIVNVASKCGMTNSNYAEMNQLYEKYKDQGLEILAFPCNQFGEEEPGTNDQITDFVCTRFKSEFPIFDKIDVNGENASPLYRFLKLGKWGIFGDDIQWNFAKFLVNKDGQVVDRYYPTTSPLSLERDIKQLLEI 169
               SCOP domains d2p5rb_ B: automated matches                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------GSHPx-2p5rB01 B:12-120                                                                                       ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------GSHPx-2p5rB02 B:12-120                                                                                       ------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhh.eee.....eee.hhhh..eeeeeee.......hhhhhhhhhhhhhhh...eeeeeee........................................hhhhhhhhhhhhhh..........eeee.....eeeee....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p5r B   6 SKNPESVHDFTVKDAKENDVDLSIFKGKVLLIVNVASKCGMTNSNYAEMNQLYEKYKDQGLEILAFPCNQFGEEEPGTNDQITDFVCTRFKSEFPIFDKIDVNGENASPLYRFLKLGKWGIFGDDIQWNFAKFLVNKDGQVVDRYYPTTSPLSLERDIKQLLEI 169
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P5R)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A3FNZ8_9ROSI | A3FNZ8)
molecular function
    GO:0004602    glutathione peroxidase activity    Catalysis of the reaction: 2 glutathione + hydrogen peroxide = oxidized glutathione + 2 H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    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: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:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2p5r)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2p5r)
 

(-) 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
  2p5r
    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
  A3FNZ8_9ROSI | A3FNZ8
    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)
  1.11.1.-
    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
  A3FNZ8_9ROSI | A3FNZ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A3FNZ8_9ROSI | A3FNZ8: 2p5q

(-) Related Entries Specified in the PDB File

2p5q