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
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOLO FORM OF GLUTAREDOXIN C1 FROM POPULUS TREMULA X TREMULOIDES
 
Authors :  H. Unno, T. Takahashi, T. Kawakami, S. Aimoto, T. Hase, M. Kusunoki, N. R J. P. Jacquot
Date :  12 Jan 07  (Deposition) - 25 Sep 07  (Release) - 07 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  D  (1x)
Keywords :  Thioredoxin Fold, Glutaredoxin, Poplar, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Rouhier, H. Unno, S. Bandyopadhyay, L. Masip, S. K. Kim, M. Hirasawa J. M. Gualberto, V. Lattard, M. Kusunoki, D. B. Knaff, G. Georgiou, T. Hase, M. K. Johnson, J. P. Jacquot
Functional, Structural, And Spectroscopic Characterization Of A Glutathione-Ligated [2Fe-2S] Cluster In Poplar Glutaredoxin C1
Proc. Natl. Acad. Sci. Usa V. 104 7379 2007
PubMed-ID: 17460036  |  Reference-DOI: 10.1073/PNAS.0702268104

(-) Compounds

Molecule 1 - GLUTAREDOXIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-3D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-116
    Organism Scientific: POPULUS TREMULA X POPULUS TREMULOIDES
    Organism Taxid: 47664

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH4Ligand/IonGLUTATHIONE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH4Ligand/IonGLUTATHIONE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH1Ligand/IonGLUTATHIONE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FES-1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH1Ligand/IonGLUTATHIONE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FES-1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH1Ligand/IonGLUTATHIONE
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1FES-1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2GSH1Ligand/IonGLUTATHIONE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:30 , GLY A:31 , GSH A:1001 , CYS C:30 , GLY C:31 , TYR C:32 , GSH C:1000BINDING SITE FOR RESIDUE FES A 1201
2AC2SOFTWARELYS A:27 , CYS A:30 , GLN A:62 , THR A:73 , VAL A:74 , PRO A:75 , GLY A:86 , CYS A:87 , ASP A:88 , FES A:1201 , HOH A:1208 , HOH A:1209 , HOH A:1214 , HOH A:1217 , HOH A:1227 , HOH A:1238 , GLY C:31 , HOH C:1002 , HOH C:1031BINDING SITE FOR RESIDUE GSH A 1001
3AC3SOFTWARETHR A:73 , LYS B:27 , CYS B:30 , TYR B:32 , GLN B:62 , THR B:73 , VAL B:74 , PRO B:75 , GLY B:86 , CYS B:87 , ASP B:88 , HOH B:1015 , HOH B:1033 , HOH B:1047 , ASN C:34 , HOH C:1031 , HOH C:1065BINDING SITE FOR RESIDUE GSH B 1002
4AC4SOFTWAREGLY A:31 , FES A:1201 , HOH A:1244 , LYS C:27 , TYR C:29 , CYS C:30 , GLN C:62 , THR C:73 , VAL C:74 , PRO C:75 , GLY C:86 , CYS C:87 , ASP C:88 , HOH C:1038 , HOH C:1063 , HOH C:1089 , HOH C:1095 , THR D:73 , GSH D:1003BINDING SITE FOR RESIDUE GSH C 1000
5AC5SOFTWARETHR A:28 , ASN A:34 , HOH A:1244 , GSH C:1000 , LYS D:27 , CYS D:30 , TYR D:32 , GLN D:62 , THR D:73 , VAL D:74 , PRO D:75 , GLY D:86 , CYS D:87 , ASP D:88 , HOH D:1004 , HOH D:1031 , HOH D:1040 , HOH D:1043BINDING SITE FOR RESIDUE GSH D 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E7P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:74 -Pro A:75
2Val B:74 -Pro B:75
3Val C:74 -Pro C:75
4Val D:74 -Pro D:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E7P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E7P)

(-) Exons   (0, 0)

(no "Exon" information available for 2E7P)

(-) 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:107
 aligned with Q5PSJ1_9ROSI | Q5PSJ1 from UniProtKB/TrEMBL  Length:126

    Alignment length:107
                                    21        31        41        51        61        71        81        91       101       111       
         Q5PSJ1_9ROSI    12 SKQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAA 118
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh...eeee.hhh.hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2e7p A   2 SKQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAA 108
                                    11        21        31        41        51        61        71        81        91       101       


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with Q5PSJ1_9ROSI | Q5PSJ1 from UniProtKB/TrEMBL  Length:126

    Alignment length:111
                                    22        32        42        52        62        72        82        92       102       112       122 
         Q5PSJ1_9ROSI    13 KQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAATAKTS 123
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh....eeee.hhh.hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2e7p B   3 KQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAATAKTS 113
                                    12        22        32        42        52        62        72        82        92       102       112 


Chain C from PDB  Type:PROTEIN  Length:115
 aligned with Q5PSJ1_9ROSI | Q5PSJ1 from UniProtKB/TrEMBL  Length:126

    Alignment length:115
                                    21        31        41        51        61        71        81        91       101       111       121     
         Q5PSJ1_9ROSI    12 SKQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAATAKTSAQL 126
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh....eeee.hhh.hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2e7p C   2 SKQELDAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAAATAKTSAQL 116
                                    11        21        31        41        51        61        71        81        91       101       111     


Chain D from PDB  Type:PROTEIN  Length:101
 aligned with Q5PSJ1_9ROSI | Q5PSJ1 from UniProtKB/TrEMBL  Length:126

    Alignment length:101
                                    26        36        46        56        66        76        86        96       106       116 
         Q5PSJ1_9ROSI    17 DAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAA 117
               SCOP domains d2e7pd_ D: automated matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh....eeee.hhh.hhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhh.hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2e7p D   7 DAALKKAKELASSAPVVVFSKTYCGYCNRVKQLLTQVGASYKVVELDELSDGSQLQSALAHWTGRGTVPNVFIGGKQIGGCDTVVEKHQRNELLPLLQDAA 107
                                    16        26        36        46        56        66        76        86        96       106
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E7P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E7P)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5PSJ1_9ROSI | Q5PSJ1)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 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
    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 ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Val A:74 - Pro A:75   [ RasMol ]  
    Val B:74 - Pro B:75   [ RasMol ]  
    Val C:74 - Pro C:75   [ RasMol ]  
    Val D:74 - Pro D:75   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ 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 | Biol. Unit 4 PNG format | Biol. Unit 5 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
  2e7p
    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
  Q5PSJ1_9ROSI | Q5PSJ1
    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)
  (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
  Q5PSJ1_9ROSI | Q5PSJ1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5PSJ1_9ROSI | Q5PSJ1: 1z7p 1z7r

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2E7P)