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 PEROXIREDOXIN 5 FROM ALVINELLA POMPEJANA
 
Authors :  A. Smeets, J. P. Declercq
Date :  15 Jun 10  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Antioxidant Enzymes (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Smeets, B. Knoops, J. P. Declercq
Crystal Structure Of Peroxiredoxin 5 From Alvinella Pompejana
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEROXIREDOXIN 5
    Chains: A, B
    EC Number: 1.11.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector: PQE-30
    Expression System Vector Type: PLASMID
    Organism Scientific: ALVINELLA POMPEJANA
    Organism Taxid: 6376

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2XHF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:175 -Pro A:176
2Glu B:175 -Pro B:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XHF)

(-) 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:156
 aligned with G1K3P1_9ANNE | G1K3P1 from UniProtKB/TrEMBL  Length:81

    Alignment length:156
                                                                                                            1                                                                           
                                     -         -         -         -         -         -         -         -|       10        20        30        40        50        60        70      
         G1K3P1_9ANNE     - --------------------------------------------------------------------------------MAAWGKTVDPEHKIRMLADMHGEFTRALGTELDSSKMLGNNRSRRYAMLIDDNKIRSVSTEPDITGLACLLSIQRQ  76
               SCOP domains d2xhfa_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eee......eeehhhhhh..eeeeee...........hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeee...hhhhhhhh....hhhhhh......eeeeee..eeeeeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xhf A  35 GSPIKVGDIIPDVLVYEDVPSKSFPIHDVFRGRKGILFSVVGAFVPGSNNHIPEYLSLYDKFKEEGYHTIACIAVNDPFVMAAWGKTVDPEHKIRMLADMHGEFTRALGTELDSSKMLGNNRSRRYAMLIDDNKIRSVSTEPDITGLACLLSIQRQ 190
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184      


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with G1K3P1_9ANNE | G1K3P1 from UniProtKB/TrEMBL  Length:81

    Alignment length:154
                                                                                                          1                                                                           
                                     -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72    
         G1K3P1_9ANNE     - ------------------------------------------------------------------------------MAAWGKTVDPEHKIRMLADMHGEFTRALGTELDSSKMLGNNRSRRYAMLIDDNKIRSVSTEPDITGLACLLSIQRQ  76
               SCOP domains d2xhfb_ B: automated matches                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee......eeehhhhhh..eeeeee...........hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeee...hhhhhhhh....hhhhhh......eeeeee..eeeeeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xhf B  37 PIKVGDIIPDVLVYEDVPSKSFPIHDVFRGRKGILFSVVGAFVPGSNNHIPEYLSLYDKFKEEGYHTIACIAVNDPFVMAAWGKTVDPEHKIRMLADMHGEFTRALGTELDSSKMLGNNRSRRYAMLIDDNKIRSVSTEPDITGLACLLSIQRQ 190
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186
   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 2XHF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G1K3P1_9ANNE | G1K3P1)
molecular function
    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:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
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.

 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
(no "Ligands, Modified Residues, Ions" information available for 2xhf)
 
  Sites
(no "Sites" information available for 2xhf)
 
  Cis Peptide Bonds
    Glu A:175 - Pro A:176   [ RasMol ]  
    Glu B:175 - Pro B:176   [ 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 ](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
  2xhf
    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
  G1K3P1_9ANNE | G1K3P1
    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)
  1.11.1.15
    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
  G1K3P1_9ANNE | G1K3P1
    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 2XHF)

(-) Related Entries Specified in the PDB File

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