Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED SCHISTOSOMA MANSONI THIOREDOXIN PRE-PROTEIN AT 1.7 ANGSTROM
 
Authors :  G. Boumis, A. E. Miele, D. Dimastrogiovanni, F. Angelucci, A. Bellelli
Date :  14 Apr 10  (Deposition) - 21 Jul 10  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Juvenile Stages, Oxidoreductase, Protein Disulfide Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Boumis, F. Angelucci, A. Bellelli, M. Brunori, D. Dimastrogiovanni, A. E. Miele
Structural And Functional Characterization Of Schistosoma Mansoni Thioredoxin.
Protein Sci. V. 20 1069 2011
PubMed-ID: 21465612  |  Reference-DOI: 10.1002/PRO.634
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN
    Chains: A, B
    EC Number: 1.8.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Common: BLOOD FLUKE
    Organism Scientific: SCHISTOSOMA MANSONI
    Organism Taxid: 6183
    Other Details: CDNA FROM ADULT SCHISTOSOMA MANSONI

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:3 , HIS A:20 , GLU B:3 , HIS B:20BINDING SITE FOR RESIDUE ZN A1107
2AC2SOFTWAREILE A:106 , HOH A:2062 , ILE B:106BINDING SITE FOR RESIDUE ZN A1108

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:75 -Pro A:76
2Met B:75 -Pro B:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XBQ)

(-) Sequences/Alignments

Asymmetric 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:105
 aligned with Q8T9N5_SCHMA | Q8T9N5 from UniProtKB/TrEMBL  Length:106

    Alignment length:105
                                    11        21        31        41        51        61        71        81        91       101     
         Q8T9N5_SCHMA     2 SKLIELKQDGDLESLLEQHKNKLVVVDFFATWCGPCKTIAPLFKELSEKYDAIFVKVDVDKLEETARKYNISAMPTFIAIKNGEKVGDVVGASIAKVEDMIKKFI 106
               SCOP domains d2xbqa_ A: automated matches                                                                              SCOP domains
               CATH domains 2xbqA00 A:2-106 Glutaredoxin                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2xbq A   2 SELIELKQDGDLESLLEQHKNKLVVVDFFATWCGPCKTIAPLFKELSEKYDAIFVKVDVDKLEETARKYNISAMPTFIAIKNGEKVGDVVGASIAKVEDMIKKFI 106
                                    11        21        31        41        51        61        71        81        91       101     


Chain B from PDB  Type:PROTEIN  Length:105
 aligned with Q8T9N5_SCHMA | Q8T9N5 from UniProtKB/TrEMBL  Length:106

    Alignment length:105
                                    11        21        31        41        51        61        71        81        91       101     
         Q8T9N5_SCHMA     2 SKLIELKQDGDLESLLEQHKNKLVVVDFFATWCGPCKTIAPLFKELSEKYDAIFVKVDVDKLEETARKYNISAMPTFIAIKNGEKVGDVVGASIAKVEDMIKKFI 106
               SCOP domains d2xbqb_ B: automated matches                                                                              SCOP domains
               CATH domains 2xbqB00 B:2-106 Glutaredoxin                                                                              CATH domains
           Pfam domains (1) ---Thioredoxin-2xbqB01 B:5-105                                                                          - Pfam domains (1)
           Pfam domains (2) ---Thioredoxin-2xbqB02 B:5-105                                                                          - Pfam domains (2)
         Sec.struct. author .eeee....hhhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 2xbq B   2 SELIELKQDGDLESLLEQHKNKLVVVDFFATWCGPCKTIAPLFKELSEKYDAIFVKVDVDKLEETARKYNISAMPTFIAIKNGEKVGDVVGASIAKVEDMIKKFI 106
                                    11        21        31        41        51        61        71        81        91       101
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8T9N5_SCHMA | Q8T9N5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016671    oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces disulfide.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0034599    cellular response to oxidative 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 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.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    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: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:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Met A:75 - Pro A:76   [ RasMol ]  
    Met B:75 - Pro B:76   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 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
  2xbq
    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
  Q8T9N5_SCHMA | Q8T9N5
    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)
  1.8.1.8
    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
  Q8T9N5_SCHMA | Q8T9N5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8T9N5_SCHMA | Q8T9N5: 2xbi 2xc2

(-) Related Entries Specified in the PDB File

2xbi CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI THIOREDOXIN AT 1.6 ANGSTROM