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 THIO-DISULFIDE ISOMERASE FROM THERMUS THERMOPHILUS
 
Authors :  Y. Patskovsky, R. Toro, J. Freeman, S. Chang, J. M. Sauder, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgx
Date :  13 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Disulfide Isomerase, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, J. Freeman, S. Chang, J. M. Sauder, S. K. Burley S. C. Almo
Crystal Structure Of Thio-Disulfide Isomerase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIO-DISULFIDE ISOMERASE/THIOREDOXIN
    Atcc: BAA-163 / DSM 7039
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)-CODON+RIL(STRATAGENE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TT_C1822
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:24 , PHE A:119 , LYS A:120 , HOH A:256BINDING SITE FOR RESIDUE ACT A 1
2AC2SOFTWAREPHE B:119 , LYS B:120 , HOH B:176BINDING SITE FOR RESIDUE ACT B 1

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:56 -A:59
2B:56 -B:59

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:45 -Pro A:46
2Gln A:124 -Pro A:125
3Lys B:45 -Pro B:46
4Gln B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IA1)

(-) Exons   (0, 0)

(no "Exon" information available for 3IA1)

(-) 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:143
 aligned with Q72GM6_THET2 | Q72GM6 from UniProtKB/TrEMBL  Length:161

    Alignment length:143
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157   
         Q72GM6_THET2    18 AVKPGEPLPDFLLLDPKGQPVTPATMSKPAVIVFWASWCTVCKAEFPGLHRVAEETGVPFYVISREPRDTREVVLEYMKAYPRFIPLLASDRDRPHEVAARFKVLGQPWTFVVDREGKVVALFAGRAGREALLDALLLAGADL 160
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.....ee.....ee........eeeeee...hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh....eee.......hhhhhhh........eeeee....eeeeeee...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ia1 A  18 AVKPGEPLPDFLLLDPKGQPVTPATVSKPAVIVFWASWCTVCKAEFPGLHRVAEETGVPFYVISREPRDTREVVLEYMKTYPRFIPLLASDRDRPHEVAARFKVLGQPWTFVVDREGKVVALFAGRAGREALLDALLLAGADL 160
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157   


Chain B from PDB  Type:PROTEIN  Length:142
 aligned with Q72GM6_THET2 | Q72GM6 from UniProtKB/TrEMBL  Length:161

    Alignment length:142
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158  
         Q72GM6_THET2    19 VKPGEPLPDFLLLDPKGQPVTPATMSKPAVIVFWASWCTVCKAEFPGLHRVAEETGVPFYVISREPRDTREVVLEYMKAYPRFIPLLASDRDRPHEVAARFKVLGQPWTFVVDREGKVVALFAGRAGREALLDALLLAGADL 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....ee.....ee........eeeeee...hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh.....ee.......hhhhhhh........eeeee....eeeeeee...hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ia1 B  19 VKPGEPLPDFLLLDPKGQPVTPATVSKPAVIVFWASWCTVCKAEFPGLHRVAEETGVPFYVISREPRDTREVVLEYMKTYPRFIPLLASDRDRPHEVAARFKVLGQPWTFVVDREGKVVALFAGRAGREALLDALLLAGADL 160
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158
   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 3IA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IA1)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q72GM6_THET2 | Q72GM6)
molecular function
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    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.
biological process
    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: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.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gln A:124 - Pro A:125   [ RasMol ]  
    Gln B:124 - Pro B:125   [ RasMol ]  
    Lys A:45 - Pro A:46   [ RasMol ]  
    Lys B:45 - Pro B:46   [ 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
  3ia1
    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
  Q72GM6_THET2 | Q72GM6
    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
  Q72GM6_THET2 | Q72GM6
    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 3IA1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3IA1)