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
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)

(-) Description

Title :  PUTATIVE THIOREDOXIN PROTEIN FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  18 Jan 11  (Deposition) - 09 Feb 11  (Release) - 09 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Csgid, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Ybbn, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
Putative Thioredoxin Protein From Salmonella Typhimurium.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE THIOREDOXIN PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Collection: 469008
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: STM0504, YBBN
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Strain: LT2

 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:281 , TYR A:284 , HOH A:325BINDING SITE FOR RESIDUE CA A 501
2AC2SOFTWAREGLN A:177 , ASP A:180 , HOH A:309BINDING SITE FOR RESIDUE CA A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:78 -Pro A:79
2Asp B:64 -Ala B:65
3Ile B:78 -Pro B:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QDN)

(-) Exons   (0, 0)

(no "Exon" information available for 3QDN)

(-) 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:285
 aligned with Q8ZR92_SALTY | Q8ZR92 from UniProtKB/TrEMBL  Length:284

    Alignment length:285
                             1                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     
         Q8ZR92_SALTY     - -MSVQNIVNINESNLQQTLEQSMTTPVLFYFWSERSQHCLQLTPVLESLAAQYHGQFILAKLDCDAEQMIAAQFGLRAIPTVYLFQNGQPVDGFQGPQPEEAIRALLDKVLPREEELKAQQAMQLMQEGNYIDALPLLKDAWQLSSQNSEIGLLLAEAQIALNRSEEAEAVLKTIPLQDQDTRYQGLVAQIELLKQAADTPEIQQLQQQVADNPQDAALATQLALQLHQVGRNEEALELLFSHLRKDLTAAEGQTRKTFQEILAALGTGDALASKYRRQLYALLY 284
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhh.......eeeeee..eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qdn A   0 AmSVQNIVNINESNLQQTLEQSmTTPVLFYFWSERSQHCLQLTPVLESLAAQYHGQFILAKLDCDAEQmIAAQFGLRAIPTVYLFQNGQPVDGFQGPQPEEAIRALLDKVLPREEELKAQQAmQLmQEGNYIDALPLLKDAWQLSSQNSEIGLLLAEAQIALNRSEEAEAVLKTIPLQDQDTRYQGLVAQIELLKQAADTPEIQQLQQQVADNPQDAALATQLALQLHQVGRNEEALELLFSHLRKDLTAAEGQTRKTFQEILAALGTGDALASKYRRQLYALLY 284
                             |       9        19  |     29        39        49        59        69        79        89        99       109       119  |  | 129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279     
                             |                   22-MSE                                        68-MSE                                               122-MSE                                                                                                                                                              
                             1-MSE                                                                                                                     125-MSE                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q8ZR92_SALTY | Q8ZR92 from UniProtKB/TrEMBL  Length:284

    Alignment length:282
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
         Q8ZR92_SALTY     3 VQNIVNINESNLQQTLEQSMTTPVLFYFWSERSQHCLQLTPVLESLAAQYHGQFILAKLDCDAEQMIAAQFGLRAIPTVYLFQNGQPVDGFQGPQPEEAIRALLDKVLPREEELKAQQAMQLMQEGNYIDALPLLKDAWQLSSQNSEIGLLLAEAQIALNRSEEAEAVLKTIPLQDQDTRYQGLVAQIELLKQAADTPEIQQLQQQVADNPQDAALATQLALQLHQVGRNEEALELLFSHLRKDLTAAEGQTRKTFQEILAALGTGDALASKYRRQLYALLY 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Thioredoxin-3qdnB01 B:5-109                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Thioredoxin-3qdnB02 B:5-109                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eee....hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh--...eeeeee...hhhhhhhhh.....eeeeee..eeee......hhhhhhhhh.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qdn B   3 VQNIVNINESNLQQTLEQSmTTPVLFYFWSERSQHCLQLTPVLESLAAQ--GQFILAKLDCDAEQmIAAQFGLRAIPTVYLFQNGQPVDGFQGPQPEEAIRALLDKVLPREEELKAQQAmQLmQEGNYIDALPLLKDAWQLSSQNSEIGLLLAEAQIALNRSEEAEAVLKTIPLQDQDTRYQGLVAQIELLKQAADTPEIQQLQQQVADNPQDAALATQLALQLHQVGRNEEALELLFSHLRKDLTAAEGQTRKTFQEILAALGTGDALASKYRRQLYALLY 284
                                    12        22        32        42        |- |      62     |  72        82        92       102       112       122  |    132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282  
                                              22-MSE                       51 54            68-MSE                                               122-MSE                                                                                                                                                              
                                                                                                                                                    125-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3QDN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QDN)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8ZR92_SALTY | Q8ZR92)
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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp B:64 - Ala B:65   [ RasMol ]  
    Ile A:78 - Pro A:79   [ RasMol ]  
    Ile B:78 - Pro B:79   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  3qdn
    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
  Q8ZR92_SALTY | Q8ZR92
    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
  Q8ZR92_SALTY | Q8ZR92
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3QDN)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3QDN)