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 :  SUPEROXIDE REDUCTASE (NEELAREDOXIN) FROM ARCHAEOGLOBUS FULGIDUS E12V IN THE REDUCED FORM
 
Authors :  T. M. Bandeiras, J. V. Rodrigues, C. M. Sousa, A. R. Barradas, F. G. Pinho A. F. Pinto, M. Teixeira, P. M. Matias, C. V. Romao
Date :  03 Sep 13  (Deposition) - 23 Jul 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Oxygen Detoxification (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Bandeiras, J. V. Rodrigues, C. M. Sousa, A. R. Barradas, F. G. Pinho, A. F. Pinto, M. Teixeira, P. M. Matias, C. V. Romao
Understanding The Role Of Key Residues In The Superoxide Reductase Molecular Mechanism, Exploring Archaeoglobus Fulgidus Sor Structure
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPEROXIDE REDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PT7-7/NAFE12VA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: SOR

 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, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FE22Ligand/IonFE (II) ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FE21Ligand/IonFE (II) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FE21Ligand/IonFE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:14 , HIS A:40 , HIS A:46 , CYS A:110 , HIS A:113BINDING SITE FOR RESIDUE FE2 A1001
2AC2SOFTWAREHIS B:14 , HIS B:40 , HIS B:46 , CYS B:110 , HIS B:113BINDING SITE FOR RESIDUE FE2 B1001
3AC3SOFTWARETHR A:6 , LYS A:11 , HOH A:2001BINDING SITE FOR RESIDUE EDO A1126
4AC4SOFTWAREALA A:72 , ALA A:73 , HIS A:74 , ALA A:76 , ASN A:111 , HOH A:2020BINDING SITE FOR RESIDUE EDO A1127
5AC5SOFTWARETYR A:64 , HIS B:74 , GLY B:75 , ALA B:76 , ASN B:111BINDING SITE FOR RESIDUE EDO B1126

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C4B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C4B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C4B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C4B)

(-) Exons   (0, 0)

(no "Exon" information available for 4C4B)

(-) 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:125
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            SOR_ARCFU     1 MELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhheeeeeeehhh.eeeeeeee.............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c4b A   1 MELFQTADWKKVKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120     


Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SOR_ARCFU | O29903 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            SOR_ARCFU     1 MELFQTADWKKEKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh...eeeeeehhh.eeeeeee..............eeeeeeeeee......eeeeeeee...............ee..eeeeeee....eeeeeeeee...eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c4b B   1 MELFQTADWKKVKHVPVIEVLRAEGGVVEVKVSVGKEIPHPNTTEHHIAWIELVFQPEGSKFPYVVGRAEFAAHGASVDGPNTSGVYTDPVAVFAFKAEKSGKLTAFSYCNIHGLWMGEATLSLE 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 4C4B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C4B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C4B)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SOR_ARCFU | O29903)
molecular function
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0050605    superoxide reductase activity    Catalysis of the reaction: superoxide + reduced rubredoxin + 2 H+ = H2O2 + rubredoxin.
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 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE2  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c4b)
 
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
  4c4b
    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
  SOR_ARCFU | O29903
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  SOR_ARCFU | O29903
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SOR_ARCFU | O29903: 4bff 4bfj 4bfk 4bgl 4c4u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4C4B)