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(-) Description

Title :  X-RAY STRUCTURE OF PMSOD2, SUPEROXIDE DISMUTASE FROM PERKINSUS 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 :  2.50
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 - IRON SUPEROXIDE DISMUTASE
    ChainsA, B
    EC Number1.15.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPERKINSUS MARINUS
    Organism Taxid31276
    SynonymPMSOD2

 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:81 , ASP A:169 , HIS A:173 , HOH A:622BINDING SITE FOR RESIDUE FE A 524
2AC2SOFTWAREHIS B:31 , HIS B:81 , ASP B:169 , HIS B:173 , HOH B:540BINDING SITE FOR RESIDUE FE B 539

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CW3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:20 -Pro A:21
2Arg B:9 -Met B:10
3Glu B:20 -Pro B:21

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CW3)

(-) Exons   (0, 0)

(no "Exon" information available for 2CW3)

(-) 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:200
 aligned with Q8ISI9_9ALVE | Q8ISI9 from UniProtKB/TrEMBL  Length:280

    Alignment length:200
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275
         Q8ISI9_9ALVE    76 PSSGLRMTLPYGLEALEPVISAATVDFHYNKHHQGYIQKLLDATGLPESRINLKSLVTLGPDRAGENVFNAAGQIYNHNMYWLSMVPTSGSGRHVPPRLLKLIRARWGNVDEMKENFMRKATALFGSGWIWLVWDTRERRLDLVGTKDAHSPLSEDAGKIPLFTCDVWEHAYYLDYQHDRAAYLTRWWSLINWEFADSNL 275
               SCOP domains d2cw3a1 A:4-90 automated matches                                                       d2cw3a2 A:91-203 automated matches                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cw3 A   4 PSSGLRMTLPYGLEALEPVISAATVDFHYNKHHQGYIQKLLDATGLPESRINLKSLVTLGPDRAGENVFNAAGQIYNHNMYWLSMVPTSGSGRHVPPRLLKLIRARWGNVDEMKENFMRKATALFGSGWIWLVWDTRERRLDLVGTKDAHSPLSEDAGKIPLFTCDVWEHAYYLDYQHDRAAYLTRWWSLINWEFADSNL 203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with Q8ISI9_9ALVE | Q8ISI9 from UniProtKB/TrEMBL  Length:280

    Alignment length:196
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269      
         Q8ISI9_9ALVE    80 LRMTLPYGLEALEPVISAATVDFHYNKHHQGYIQKLLDATGLPESRINLKSLVTLGPDRAGENVFNAAGQIYNHNMYWLSMVPTSGSGRHVPPRLLKLIRARWGNVDEMKENFMRKATALFGSGWIWLVWDTRERRLDLVGTKDAHSPLSEDAGKIPLFTCDVWEHAYYLDYQHDRAAYLTRWWSLINWEFADSNL 275
               SCOP domains d2cw3b1 B:8-90 automated matches                                                   d2cw3b2 B:91-203 automated matches                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....eeeeeeee...hhhhhh..eeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cw3 B   8 LRMTLPYGLEALEPVISAATVDFHYNKHHQGYIQKLLDATGLPESRINLKSLVTLGPDRAGENVFNAAGQIYNHNMYWLSMVPTSGSGRHVPPRLLKLIRARWGNVDEMKENFMRKATALFGSGWIWLVWDTRERRLDLVGTKDAHSPLSEDAGKIPLFTCDVWEHAYYLDYQHDRAAYLTRWWSLINWEFADSNL 203
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197      

   Legend:   → Mismatch (orange background)
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  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 2CW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CW3)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ISI9_9ALVE | Q8ISI9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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(-) Related Entries Specified in the PDB File

2cw2 SUPEROXIDE DISMUTASE 1