Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 SUPEROXIDE DISMUTASE FROM P. MARINUS
 
Authors :  O. A. Asojo, E. J. Schott, G. R. Vasta, A. M. Silva
Date :  16 Jun 05  (Deposition) - 04 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sod, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. A. Asojo, E. J. Schott, G. R. Vasta, A. M. Silva
Structures Of Pmsod1 And Pmsod2, Two Superoxide Dismutases From The Protozoan Parasite Perkinsus Marinus
Acta Crystallogr. , Sect. F V. 62 1072 2006
PubMed-ID: 17077482  |  Reference-DOI: 10.1107/S1744309106040425
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE 1
    ChainsA, B
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPBLUESCRIPTII
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPERKINSUS MARINUS
    Organism Taxid31276

 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
1FE2Ligand/IonFE (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:31 , HIS A:80 , ASP A:162 , HIS A:166 , HOH A:505BINDING SITE FOR RESIDUE FE A 402
2AC2SOFTWAREHIS B:31 , HIS B:80 , ASP B:162 , HIS B:166 , HOH B:497BINDING SITE FOR RESIDUE FE B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CW2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:5 -Pro A:6
2Glu A:20 -Pro A:21
3Gly B:5 -Pro B:6
4Glu B:20 -Pro B:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CW2)

(-) Exons   (0, 0)

(no "Exon" information available for 2CW2)

(-) 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:199
 aligned with Q8ISJ0_9ALVE | Q8ISJ0 from UniProtKB/TrEMBL  Length:226

    Alignment length:199
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217         
         Q8ISJ0_9ALVE    28 SVTGPFQCPPLPYVKNALEPHMSAETLTYHHDKHHQTYVDTLNSIAAENSTIASKTLEQIIKTETGKPFNQAAQVYNHTFFFNNLAPNGGGEPTGKIAELITRDFGSFEKFKEDFSAAAVGHFGSGWVWLIADDGKLKIVQGHDAGNPIRESKTPLMNIDVWEHAYYIDYRNARAQYVKNYWNLVNWDFVNDNVAKAGI 226
               SCOP domains d2cw2a1 A:2-89 automated matches                                                       d2cw2a2 A:90-201 automated matches                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeee...hhhhh..eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cw2 A   2 SVTGPFQCPPLPYVKNALEPHMSAETLTYHHDKHHQTYVDTLNSIAAENSTIASKTLEQIIKTETGKPFNQAAQVYNHTFFFNNLAPNGGGEPTGKIAELITRDFGSFEKFKEDFSAAAVGHFGSGWVWLIADDGKLKIVQGHDAGNPIRESKTPLMNIDVWEHAYYIDYRNARAQYVKNYWNLVNWDFVNDNVAKAGI 201
                                    11        21        31        41        51 ||     62        72        82        92       102       112       122       132       142       152       162       172       182       192         
                                                                              53|                                                                                                                                                  
                                                                               55                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q8ISJ0_9ALVE | Q8ISJ0 from UniProtKB/TrEMBL  Length:226

    Alignment length:196
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
         Q8ISJ0_9ALVE    31 GPFQCPPLPYVKNALEPHMSAETLTYHHDKHHQTYVDTLNSIAAENSTIASKTLEQIIKTETGKPFNQAAQVYNHTFFFNNLAPNGGGEPTGKIAELITRDFGSFEKFKEDFSAAAVGHFGSGWVWLIADDGKLKIVQGHDAGNPIRESKTPLMNIDVWEHAYYIDYRNARAQYVKNYWNLVNWDFVNDNVAKAGI 226
               SCOP domains d2cw2b1 B:5-89 automated matches                                                    d2cw2b2 B:90-201 automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeee...hhhhhh.eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cw2 B   5 GPFQCPPLPYVKNALEPHMSAETLTYHHDKHHQTYVDTLNSIAAENSTIASKTLEQIIKTETGKPFNQAAQVYNHTFFFNNLAPNGGGEPTGKIAELITRDFGSFEKFKEDFSAAAVGHFGSGWVWLIADDGKLKIVQGHDAGNPIRESKTPLMNIDVWEHAYYIDYRNARAQYVKNYWNLVNWDFVNDNVAKAGI 201
                                    14        24        34        44        54 ||     65        75        85        95       105       115       125       135       145       155       165       175       185       195      
                                                                              56|                                                                                                                                               
                                                                               58                                                                                                                                               

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CW2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ISJ0_9ALVE | Q8ISJ0)
molecular function
    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:0004784    superoxide dismutase activity    Catalysis of the reaction: 2 superoxide + 2 H+ = O2 + hydrogen peroxide.
biological process
    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:0019430    removal of superoxide radicals    Any process, acting at the cellular level, involved in removing superoxide radicals (O2-) from a cell or organism, e.g. by conversion to dioxygen (O2) and hydrogen peroxide (H2O2).
    GO:0006801    superoxide metabolic process    The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species.

 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
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:20 - Pro A:21   [ RasMol ]  
    Glu B:20 - Pro B:21   [ RasMol ]  
    Gly A:5 - Pro A:6   [ RasMol ]  
    Gly B:5 - Pro B:6   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2cw2
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8ISJ0_9ALVE | Q8ISJ0
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.15.1.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q8ISJ0_9ALVE | Q8ISJ0
    Protein Disorder PredictionDisEMBL | 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 2CW2)

(-) Related Entries Specified in the PDB File

2cw3 IRON SUPEROXIDE DISMUTASE