Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF SUPEROXIDE DISMUTASE FROM BABESIA BOVIS SOLVED BY SULFUR SAD
 
Authors :  J. W. Fairman, M. C. Clifton, J. Abendroth, T. E. Edwards, D. Lorimer, Se Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  24 Feb 15  (Deposition) - 15 Apr 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Superoxide Dismutase, Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Q. Phan, D. R. Davies, N. S. Moretti, D. Shanmugam, I. Cestari, A. Anupama, J. W. Fairman, T. E. Edwards, K. Stuart, S. Schenkman, P. J. Myler
Iron Superoxide Dismutases In Eukaryotic Pathogens: New Insights From Apicomplexa And Trypanosoma Structures.
Acta Crystallogr. , Sect. F V. 71 615 2015
PubMed-ID: 25961325  |  Reference-DOI: 10.1107/S2053230X15004185

(-) Compounds

Molecule 1 - SUPEROXIDE DISMUTASE
    Chains: A, B
    EC Number: 1.15.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FE-SOD, BBOV_IV011480
    Organism Scientific: BABESIA BOVIS
    Organism Taxid: 5865

 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:27 , HIS A:74 , ASP A:158 , HIS A:162 , HOH A:445binding site for residue FE A 300
2AC2SOFTWAREHIS B:27 , HIS B:74 , ASP B:158 , HIS B:162 , HOH B:449binding site for residue FE B 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:16 -Pro A:17
2Ile B:16 -Pro B:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YET)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...........eeeeeee.hhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yet A   2 AFKLPALPYGMRELIPHISEETLSFHYGKHHAGYVNKLNSLIKGTPMESCTIEELILGQTGAVFNNAAQIWNHTFYWNSMGPNCGGEPTGPIRKKIEEKFGSFSAFKTDFSNLLAGHFGSGWGWLVLKDDGTADIVQTHDAGSPLKENLGRPLLCCDVWEHAYYIDYKNDRLSYINSWWNLVNWDFANKNLEAPFKWS 199
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191        


Chain B from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeee...........eeeeeee.hhhhhhhhhh.hhhhhhhhhh...hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yet B   0 SMAFKLPALPYGMRELIPHISEETLSFHYGKHHAGYVNKLNSLIKGTPMESCTIEELILGQTGAVFNNAAQIWNHTFYWNSMGPNCGGEPTGPIRKKIEEKFGSFSAFKTDFSNLLAGHFGSGWGWLVLKDDGTADIVQTHDAGSPLKENLGRPLLCCDVWEHAYYIDYKNDRLSYINSWWNLVNWDFANKNLEAPFKWS 199
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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 ; only for superseded entry 4K2W: 2,4)

(no "SCOP Domain" information available for 4YET, only for superseded entry 4K2W replaced by 4YET)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    Ile A:16 - Pro A:17   [ RasMol ]  
    Ile B:16 - Pro B:17   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  4yet
    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
  O15904_BABBO | O15904
    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)
  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
  O15904_BABBO | O15904
    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 4YET)

(-) Related Entries Specified in the PDB File

4k2w THIS ENTRY SUPERSEDES ENTRY 4K2W. MORE EVIDENCE HAS SHOWN US THAT THE ZINCS PRESENT IN 4K2W SHOULD BE IRON IONS INSTEAD OF ZINCS. RELATED ID: SSGCID-BABOA.01199.A RELATED DB: TARGETTRACK