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
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)

(-) Description

Title :  P.SHERMANII SOD(FE+3) 140K PH8
 
Authors :  M. Schmidt
Date :  28 Aug 98  (Deposition) - 15 Jun 99  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Superoxide Dismutase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schmidt
Manipulating The Coordination Mumber Of The Ferric Iron Within The Cambialistic Superoxide Dismutase Of Propionibacterium Shermanii By Changing The Ph-Value A Crystallographic Analysis
Eur. J. Biochem. V. 262 117 1999
PubMed-ID: 10231372  |  Reference-DOI: 10.1046/J.1432-1327.1999.00359.X

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Atcc: GERMAN COLLECTION OF MICROORGANISMS (DSM) 4902
    Cellular Location: CYTOPLASM
    Chains: A, B
    Collection: GERMAN COLLECTION OF MICROORGANISMS (DSM) 4902
    EC Number: 1.15.1.1
    Organism Scientific: PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
    Organism Taxid: 1752
    Strain: PZ3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:27 , HIS A:75 , ASP A:161 , HIS A:165 , HOH A:203 , HOH A:204BINDING SITE FOR RESIDUE FE A 202
2AC2SOFTWAREHIS B:27 , HIS B:75 , ASP B:161 , HIS B:165 , HOH B:203 , HOH B:204BINDING SITE FOR RESIDUE FE B 202
3FEAUNKNOWNFE A:202 , HIS A:27 , HIS A:75 , ASP A:161 , HIS A:165 , HOH A:203 , HOH A:204FERRIC IRON A HEXA COORDINATED SUBSTRATE BINDING SITE BLOCKED BY A SOLVENT MOLECULE
4FEBUNKNOWNFE B:202 , HIS B:27 , HIS B:75 , ASP B:161 , HIS B:165 , HOH B:203 , HOH B:204FERRIC IRON B HEXA COORDINATED SUBSTRATE BINDING SITE BLOCKED BY A SOLVENT MOLECULE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BSM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:16 -Pro A:17
2Glu B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BSM)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_PROFR161-168
 		  2A:161-168
B:161-168
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SOD_MNPS00088 Manganese and iron superoxide dismutases signature.SODM_PROFR161-168
 		  4A:161-168
B:161-168

(-) Exons   (0, 0)

(no "Exon" information available for 1BSM)

(-) 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:201
 aligned with SODM_PROFR | P80293 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SODM_PROFR     1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
               SCOP domains d1bsma1 A:1-86 Cambialistic superoxide dismutase                                      d1bsma2 A:87-201 Cambialistic superoxide dismutase                                                                  SCOP domains
               CATH domains -------------------1bsmA01 A:20-83 Fe,Mn superoxide dismutase (SOD) domain         ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..........eeeeeee..hhh.hhhh...hhhhhhhhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsm A   1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 


Chain B from PDB  Type:PROTEIN  Length:201
 aligned with SODM_PROFR | P80293 from UniProtKB/Swiss-Prot  Length:201

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           SODM_PROFR     1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
               SCOP domains d1bsmb1 B:1-86 Cambialistic superoxide dismutase                                      d1bsmb2 B:87-201 Cambialistic superoxide dismutase                                                                  SCOP domains
               CATH domains -------------------1bsmB01 B:20-83 Fe,Mn superoxide dismutase (SOD) domain         ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....hhh......hhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeee....eeeeeeee..........eeeeeee..hhh.hhhh...hhhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------SOD_MN  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bsm B   1 AVYTLPELPYDYSALEPYISGEIMELHHDKHHKAYVDGANTALDKLAEARDKADFGAINKLEKDLAFNLAGHVNHSVFWKNMAPKGSAPERPTDELGAAIDEFFGSFDNMKAQFTAAATGIQGSGWASLVWDPLGKRINTLQFYDHQNNLPAGSIPLLQLDMWEHAFYLQYKNVKGDYVKSWWNVVNWDDVALRFSEARVA 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BSM)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SODM_PROFR | P80293)
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 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 ]
    FEA  [ RasMol ]  +environment [ RasMol ]
    FEB  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:16 - Pro A:17   [ RasMol ]  
    Glu B:16 - Pro B:17   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1bsm
    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
  SODM_PROFR | P80293
    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)
  1.15.1.1
    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
  SODM_PROFR | P80293
    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
        SODM_PROFR | P80293: 1ar4 1ar5 1avm 1bs3 1bt8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BSM)