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 :  THE CRYSTAL STRUCTURE OF A SECRETED THIOL-DISULFIDE ISOMERASE FROM CORYNEBACTERIUM GLUTAMICUM TO 1.75A
 
Authors :  A. J. Stein, A. Weger, R. Hendricks, G. Cobb, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  23 Feb 10  (Deposition) - 02 Mar 10  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Thiol-Disulfide, Isomerase, Thioredoxin, Corynebacterium, Glutamicum, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, A. Weger, R. Hendricks, G. Cobb, A. Joachimiak
The Crystal Structure Of A Secreted Thiol-Disulfide Isomerase From Corynebacterium Glutamicum To 1. 75A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SECRETED THIOL-DISULFIDE ISOMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: SEQUENCE DATABASE RESIDUES 25-187
    Gene: CG0520, CGL0439
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM
    Organism Taxid: 1718
    Strain: ATCC 13032
    Synonym: THIOL-DISULFIDE ISOMERASE, THIOREDOXINS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:221 , HOH A:222 , HOH A:223 , HOH A:224 , HOH A:225 , HOH A:226BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWARESER A:68 , LEU A:69 , MSE A:70 , SER A:151BINDING SITE FOR RESIDUE CA A 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:171 -Pro A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LWA)

(-) 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:167
 aligned with Q8NT71_CORGL | Q8NT71 from UniProtKB/TrEMBL  Length:207

    Alignment length:170
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
         Q8NT71_CORGL    37 GGTFQFHSPDGKMEIFYDEADRQQLPDIGGDSLMEEGTQINLSDFENQVVILNAWGQWCAPCRSESDDLQIIHEELQAAGNGDTPGGTVLGINVRDYSRDIAQDFVTDNGLDYPSIYDPPFMTAASLGGVPASVIPTTIVLDKQHRPAAVFLREVTSKDVLDVALPLVDE 206
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------AhpC-TSA-3lwaA01 A:58-182                                                                                                    ------------------------ Pfam domains
         Sec.struct. author .............eee.hhhhh......eee.......eee.hhhh..eeeeeee...hhhhhhhhhhhhhhhhhhhhh.---...eeeeeee....hhhhhhhhhhhh.....eee...hhhhhhh.........eeeee.....eeeee....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lwa A  37 GGTFQFHSPDGKmEIFYDEADRQQLPDIGGDSLmEEGTQINLSDFENQVVILNAWGQWCAPCRSESDDLQIIHEELQAAG---TPGGTVLGINVRDYSRDIAQDFVTDNGLDYPSIYDPPFmTAASLGGVPASVIPTTIVLDKQHRPAAVFLREVTSKDVLDVALPLVDE 206
                                    46  |     56        66   |    76        86        96       106       116   |   126       136       146       156 |     166       176       186       196       206
                                       49-MSE               70-MSE                                       116 120                                   158-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 3LWA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8NT71_CORGL | Q8NT71)
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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:171 - Pro A:172   [ 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
  3lwa
    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
  Q8NT71_CORGL | Q8NT71
    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
  Q8NT71_CORGL | Q8NT71
    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 3LWA)

(-) Related Entries Specified in the PDB File

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