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 THE HOLO FORM OF GLUTAREDOXIN C5 FROM ARABIDOPSIS THALIANA
 
Authors :  T. Roret, J. Couturier, P. Tsan, J. P. Jacquot, N. Rouhier, C. Didierjea
Date :  11 Apr 11  (Deposition) - 01 Jun 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thioredoxin Fold, Thiol-Disulfide Oxidoreductase, [2Fe-2S] Cluster, Glutaredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Couturier, E. Stroher, A. N. Albetel, T. Roret, M. Muthuramalingam L. Tarrago, T. Seidel, P. Tsan, J. P. Jacquot, M. K. Johnson, K. J. Dietz C. Didierjean, N. Rouhier
Arabidopsis Chloroplastic Glutaredoxin C5 As A Model To Explore Molecular Determinants For Iron-Sulfur Cluster Binding Into Glutaredoxins.
J. Biol. Chem. V. 286 27515 2011
PubMed-ID: 21632542  |  Reference-DOI: 10.1074/JBC.M111.228726

(-) Compounds

Molecule 1 - GLUTAREDOXIN-C5, CHLOROPLASTIC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GRXC5, AT4G28730, F16A16.160
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATGRXC5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH2Ligand/IonGLUTATHIONE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:26 , CYS A:29 , GLN A:62 , THR A:73 , VAL A:74 , GLY A:86 , CYS A:87 , THR A:88 , FES A:115 , HOH A:116 , HOH A:118 , TRP B:28 , SER B:30BINDING SITE FOR RESIDUE GSH A 114
2AC2SOFTWARECYS A:29 , TYR A:31 , GSH A:114 , CYS B:29 , TYR B:31 , GSH B:114BINDING SITE FOR RESIDUE FES A 115
3AC3SOFTWARETRP A:28 , SER A:30 , FES A:115 , LYS B:26 , CYS B:29 , TYR B:31 , GLN B:62 , THR B:73 , VAL B:74 , PRO B:75 , GLY B:86 , CYS B:87 , THR B:88 , ASP B:89 , HOH B:171BINDING SITE FOR RESIDUE GSH B 114

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RHC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:74 -Pro A:75
2Ile A:84 -Gly A:85
3Ala A:104 -Glu A:105
4Val B:74 -Pro B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.GRXC5_ARATH70-171
 		  2A:9-105
B:9-105

(-) Exons   (0, 0)

(no "Exon" information available for 3RHC)

(-) 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:103
 aligned with GRXC5_ARATH | Q8GWS0 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:103
                                    73        83        93       103       113       123       133       143       153       163   
          GRXC5_ARATH    64 SFGSRMEESIRKTVTENTVVIYSKTWCSYCTEVKTLFKRLGVQPLVVELDQLGPQGPQLQKVLERLTGQHTVPNVFVCGKHIGGCTDTVKLNRKGDLELMLAE 166
               SCOP domains d3rhca_ A: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh.....eeee..ee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------GLUTAREDOXIN_2  PDB: A:9-105 UniProt: 70-171                                                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3rhc A   3 SFGSRMEESIRKTVTENTVVIYSKTWCSYCTEVKTLFKRLGVQPLVVELDQLGPQGPQLQKVLERLTGQHTVPNVFVCGKHIGGCTDTVKLNRKGDLELMLAE 105
                                    12        22        32        42        52        62        72        82        92       102   


Chain B from PDB  Type:PROTEIN  Length:100
 aligned with GRXC5_ARATH | Q8GWS0 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:100
                                    76        86        96       106       116       126       136       146       156       166
          GRXC5_ARATH    67 SRMEESIRKTVTENTVVIYSKTWCSYCTEVKTLFKRLGVQPLVVELDQLGPQGPQLQKVLERLTGQHTVPNVFVCGKHIGGCTDTVKLNRKGDLELMLAE 166
               SCOP domains d3rhcb_ B: automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------Glutaredoxin-3rhcB01 B:21-84                                    --------------------- Pfam domains (1)
           Pfam domains (2) ---------------Glutaredoxin-3rhcB02 B:21-84                                    --------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhh.......eeee..eeeehhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---GLUTAREDOXIN_2  PDB: B:9-105 UniProt: 70-171                                                      PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3rhc B   6 SRMEESIRKTVTENTVVIYSKTWCSYCTEVKTLFKRLGVQPLVVELDQLGPQGPQLQKVLERLTGQHTVPNVFVCGKHIGGCTDTVKLNRKGDLELMLAE 105
                                    15        25        35        45        55        65        75        85        95       105
   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 3RHC)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GRXC5_ARATH | Q8GWS0)
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:0004362    glutathione-disulfide reductase activity    Catalysis of the reaction: 2 glutathione + NADP+ = glutathione disulfide + NADPH + H+.
    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:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.
    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.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

 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
    FES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GSH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:104 - Glu A:105   [ RasMol ]  
    Ile A:84 - Gly A:85   [ RasMol ]  
    Val A:74 - Pro A:75   [ RasMol ]  
    Val B:74 - Pro B:75   [ 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 | Asym./Biol. Unit - sites 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
  3rhc
    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
  GRXC5_ARATH | Q8GWS0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  GRXC5_ARATH | Q8GWS0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GRXC5_ARATH | Q8GWS0: 3rhb

(-) Related Entries Specified in the PDB File

3fz9 3rhb