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

(-) Description

Title :  CRYSTAL STRUCTURE OF THIOREDOXIN F FROM SPINACH CHLOROPLAST (SHORT FORM)
 
Authors :  G. Capitani, Z. Markovic-Housley, G. Delval, M. Morris, J. N. Jansonius, P. Schurmann
Date :  11 Jul 00  (Deposition) - 20 Sep 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Capitani, Z. Markovic-Housley, G. Delval, M. Morris, J. N. Jansonius, P. Schurmann
Crystal Structures Of Two Functionally Different Thioredoxins In Spinach Chloroplasts.
J. Mol. Biol. V. 302 135 2000
PubMed-ID: 10964566  |  Reference-DOI: 10.1006/JMBI.2000.4006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOREDOXIN F
    Cellular Location: CHLOROPLAST
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3D
    Expression System Taxid: 562
    Fragment: SHORT FORM
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F9M)

(-) Sites  (0, 0)

(no "Site" information available for 1F9M)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:46 -A:49
2B:46 -B:49

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:89 -Pro A:90
2Val B:89 -Pro B:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F9M)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TRXF_SPIOL106-124
 		  2A:38-56
B:38-56
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TRXF_SPIOL106-124
 		  1A:38-56
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.TRXF_SPIOL106-124
 		  1-
B:38-56

(-) Exons   (0, 0)

(no "Exon" information available for 1F9M)

(-) 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:112
 aligned with TRXF_SPIOL | P09856 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:112
                                    87        97       107       117       127       137       147       157       167       177       187  
           TRXF_SPIOL    78 MEAIVGKVTEVNKDTFWPIVKAAGDKPVVLDMFTQWCGPCKAMAPKYEKLAEEYLDVIFLKLDCNQENKTLAKELGIRVVPTFKILKENSVVGEVTGAKYDKLLEAIQAARS 189
               SCOP domains d1f9ma_ A: Thioredoxin                                                                                           SCOP domains
               CATH domains 1f9mA00 A:10-121 Glutaredoxin                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee...hhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhh.....eeeeee..eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1f9m A  10 MEAIVGKVTEVNKDTFWPIVKAAGDKPVVLDMFTQWCGPCKAMAPKYEKLAEEYLDVIFLKLDCNQENKTLAKELGIRVVPTFKILKENSVVGEVTGAKYDKLLEAIQAARS 121
                                    19        29        39        49        59        69        79        89        99       109       119  


Chain B from PDB  Type:PROTEIN  Length:112
 aligned with TRXF_SPIOL | P09856 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:112
                                    87        97       107       117       127       137       147       157       167       177       187  
           TRXF_SPIOL    78 MEAIVGKVTEVNKDTFWPIVKAAGDKPVVLDMFTQWCGPCKAMAPKYEKLAEEYLDVIFLKLDCNQENKTLAKELGIRVVPTFKILKENSVVGEVTGAKYDKLLEAIQAARS 189
               SCOP domains d1f9mb_ B: Thioredoxin                                                                                           SCOP domains
               CATH domains 1f9mB00 B:10-121 Glutaredoxin                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee....hhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh......eeeeee..eeeeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------THIOREDOXIN_1      ----------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1f9m B  10 MEAIVGKVTEVNKDTFWPIVKAAGDKPVVLDMFTQWCGPCKAMAPKYEKLAEEYLDVIFLKLDCNQENKTLAKELGIRVVPTFKILKENSVVGEVTGAKYDKLLEAIQAARS 121
                                    19        29        39        49        59        69        79        89        99       109       119
   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  (0, 0)

(no "Pfam Domain" information available for 1F9M)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRXF_SPIOL | P09856)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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: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.
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 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 1f9m)
 
  Sites
(no "Sites" information available for 1f9m)
 
  Cis Peptide Bonds
    Val A:89 - Pro A:90   [ RasMol ]  
    Val B:89 - Pro B:90   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 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
  1f9m
    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
  TRXF_SPIOL | P09856
    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
  TRXF_SPIOL | P09856
    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
        TRXF_SPIOL | P09856: 1faa 2pu9 2pvo

(-) Related Entries Specified in the PDB File

1faa THIOREDOXIN F FROM SPINACH CHLOROPLAST (LONG FORM)
1fb0 THIOREDOXIN M FROM SPINACH CHLOROPLAST (REDUCED FORM)
1fb6 THIOREDOXIN M FROM SPINACH CHLOROPLAST (OXIDIZED FORM)