Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD (OXIDIZED FORM)
 
Authors :  C. U. Stirnimann, A. Rozhkova, U. Grauschopf, R. A. Boeckmann, R. Glockshuber, G. Capitani, M. G. Gruetter
Date :  02 Feb 06  (Deposition) - 13 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Dsbd, Thioredoxin-Like, C-Terminal Domain, Oxidized Form, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. U. Stirnimann, A. Rozhkova, U. Grauschopf, R. A. Boeckmann, R. Glockshuber, G. Capitani, M. G. Gruetter
High-Resolution Structures Of Escherichia Coli Cdsbd In Different Redox States: A Combined Crystallographic, Biochemical And Computational Study
J. Mol. Biol. V. 358 829 2006
PubMed-ID: 16545842  |  Reference-DOI: 10.1016/J.JMB.2006.02.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIOL:DISULFIDE INTERCHANGE PROTEIN DSBD
    ChainsA
    EC Number1.8.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDSBA3
    Expression System StrainBL21 ROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, RESIDUES 419-546
    GeneDSBD, DIPZ, CYCZ, CUTA2, B4136
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymPROTEIN-DISULFIDE REDUCTASE, DISULFIDE REDUCTASE, C-TYPE CYTOCHROME BIOGENESIS PROTEIN CYCZ, INNER MEMBRANE COPPER TOLERANCE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION
2NA1Ligand/IonSODIUM ION
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:429 , GLU A:468 , GLN A:488BINDING SITE FOR RESIDUE IOD A 1001
2AC2SOFTWAREHOH A:19 , HIS A:523 , NA A:1101BINDING SITE FOR RESIDUE IOD A 1002
3AC3SOFTWAREHOH A:37 , HOH A:181 , GLN A:545 , HIS A:547BINDING SITE FOR RESIDUE IOD A 1003
4AC4SOFTWAREHOH A:127 , ASP A:438BINDING SITE FOR RESIDUE IOD A 1005
5AC5SOFTWAREHOH A:100 , HOH A:167 , LYS A:448 , GLU A:466BINDING SITE FOR RESIDUE IOD A 1006
6AC6SOFTWAREHOH A:144 , TRP A:460 , CYS A:461 , GLU A:535BINDING SITE FOR RESIDUE IOD A 1013
7AC7SOFTWAREHOH A:3 , HOH A:111 , HOH A:113 , HOH A:150 , LEU A:508 , GLY A:509BINDING SITE FOR RESIDUE IOD A 1015
8AC8SOFTWAREGLU A:446 , ASP A:483 , HIS A:547 , HIS A:548BINDING SITE FOR RESIDUE NI A 1050
9AC9SOFTWAREHOH A:77 , HOH A:126 , HIS A:523 , ARG A:544 , GLN A:545 , IOD A:1002BINDING SITE FOR RESIDUE NA A 1101

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:461 -A:464

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:510 -Pro A:511

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOREDOXIN_1PS00194 Thioredoxin family active site.DSBD_ECOLI472-490  1A:453-471

(-) Exons   (0, 0)

(no "Exon" information available for 2FWE)

(-) 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:122
 aligned with DSBD_ECOLI | P36655 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:122
                                                                                                                                                565   
                                   456       466       476       486       496       506       516       526       536       546       556        |-  
           DSBD_ECOLI   447 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQP---   -
               SCOP domains d2fwea_ A: Thiol:disulfide interchange protein DsbD, C-terminal domain (DsbD-gamma)                                        SCOP domains
               CATH domains 2fweA00 A:428-549 Glutaredoxin                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee..hhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh..hhhhhhhh...eeeeee....hhhhhhhhhhh......eeeee......hhhhh.....hhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------THIOREDOXIN_1      ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fwe A 428 HLNFTQIKTVDELNQALVEAKGKPVMLDLYADWCVACKEFEKYTFSDPQVQKALADTVLLQANVTANDAQDVALLKHLNVLGLPTILFFDGQGQEHPQARVTGFMDAETFSAHLRDRQPHHH 549
                                   437       447       457       467       477       487       497       507       517       527       537       547  

   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/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DSBD_ECOLI | P36655)
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: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:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0047134    protein-disulfide reductase activity    Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
    GO:0022865    transmembrane electron transfer carrier    Enables electron flow across a biological membrane, from donors localized on one side of the membrane to acceptors localized on the other side. These systems contribute to or subtract from the membrane potential, depending on the direction of electron flow. They are therefore important to cellular energetics.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0071502    cellular response to temperature stimulus    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 a temperature stimulus.
    GO:0017004    cytochrome complex assembly    The aggregation, arrangement and bonding together of a cytochrome complex. A cytochrome complex is a protein complex in which at least one of the proteins is a cytochrome, i.e. a heme-containing protein involved in catalysis of redox reactions.
    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:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0009898    cytoplasmic side of plasma membrane    The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
    IOD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NI  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:510 - Pro A:511   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2fwe
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DSBD_ECOLI | P36655
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.8.1.8
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  DSBD_ECOLI | P36655
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DSBD_ECOLI | P366551jpe 1jzd 1l6p 1vrs 1z5y 2fwf 2fwg 2fwh 3pfu 4ip1 4ip6

(-) Related Entries Specified in the PDB File

1vrs CRYSTAL STRUCTURE OF THE DISULFIDE-LINKED COMPLEX BETWEEN THE N-TERMINAL AND C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD
2fwf HIGH RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD (REDUCED FORM)
2fwg HIGH RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD (PHOTOREDUCED FORM)
2fwh ATOMIC RESOLUTION CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE ELECTRON TRANSFER CATALYST DSBD (REDUCED FORM AT PH7)