Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF A THIOL:DISULFIDE INTERCHANGE PROTEIN FROM BACTEROIDES SP.
 
Authors :  R. Harris, A. D. Bandaranayake, R. Banu, J. B. Bonanno, D. A. Calarese, A. Celikgil, S. Chamala, M. K. Chan, R. Chaparro, B. Evans, S. Garforth B. Hillerich, A. Kar, J. Lafleur, S. Lim, J. Love, B. Matikainen, H. Pat R. D. Seidel, B. Smith, M. Stead, M. E. Girvin, S. C. Almo, New York Str Genomics Research Consortium (Nysgrc)
Date :  10 Apr 12  (Deposition) - 25 Apr 12  (Release) - 25 Apr 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Structural Genomics, Thioredoxin-Like, New York Structural Genomics Research Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Harris, A. D. Bandaranayake, R. Banu, J. B. Bonanno, D. A. Calarese, A. Celikgil, S. Chamala, M. K. Chan, R. Chaparro, B. Evans, S. Garforth A. Gizzi, B. Hillerich, A. Kar, J. Lafleur, S. Lim, J. Love, B. Matikainen, H. Patel, R. D. Seidel, B. Smith, M. Stead, M. E. Girvin, S. C. Almo
Solution Structure Of A Thiol:Disulfide Interchange Protein From Bacteroides Sp.
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: MODIFIED PET26
    Expression System Vector Type: PET
    Fragment: UNP RESIDUES 252-392
    Gene: BSFG_02257
    Organism Scientific: BACTEROIDES SP. 4_3_47FAA
    Organism Taxid: 457394

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LRN)

(-) Sites  (0, 0)

(no "Site" information available for 2LRN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Phe A:110 -Pro A:111

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LRN)

(-) Sequences/Alignments

NMR Structure
   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:152
 aligned with C6Z5F1_9BACE | C6Z5F1 from UniProtKB/TrEMBL  Length:392

    Alignment length:152
                                                                                                                                                                         392        
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388   |     -  
         C6Z5F1_9BACE   249 ARCATGSVAPAITGIDLKGNSVSLNDFKGKYVLVDFWFAGCSWCRKETPYLLKTYNAFKDKGFTIYGVSTDRREEDWKKAIEEDKSYWNQVLLQKDDVKDVLESYCIVGFPHIILVDPEGKIVAKELRGDDLYNTVEKFVNGAK--------   -
               SCOP domains d2lrna_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eee.....eee.hhhh..eeeeeee.....hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh...eeeeehhhhhhhhhhhh......eeeee....eeeee....hhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2lrn A   1 MSLATGSVAPAITGIDLKGNSVSLNDFKGKYVLVDFWFAGCSWCRKETPYLLKTYNAFKDKGFTIYGVSTDRREEDWKKAIEEDKSYWNQVLLQKDDVKDVLESYCIVGFPHIILVDPEGKIVAKELRGDDLYNTVEKFVNGAKEGHHHHHH 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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)

NMR Structure
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A   (C6Z5F1_9BACE | C6Z5F1)
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: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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0051920    peroxiredoxin activity    Catalysis of the reaction: 2 R'-SH + ROOH = R'-S-S-R' + H2O + ROH.
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

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2lrn)
 
  Sites
(no "Sites" information available for 2lrn)
 
  Cis Peptide Bonds
    Phe A:110 - Pro A:111   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2lrn
    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
  C6Z5F1_9BACE | C6Z5F1
    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
  C6Z5F1_9BACE | C6Z5F1
    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 2LRN)

(-) Related Entries Specified in the PDB File

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