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 :  IRON-BOUND CRYSTAL STRUCTURE OF STREPTOCOCCUS PYOGENES DPR
 
Authors :  T. Haikarainen, C. -C. Tsou, J. -J. Wu, A. C. Papageorgiou
Date :  26 Jun 09  (Deposition) - 15 Sep 09  (Release) - 14 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Dna-Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Haikarainen, C. -C. Tsou, J. -J. Wu, A. C. Papageorgiou
Crystal Structures Of Streptococcus Pyogenes Dpr Reveal A Dodecameric Iron-Binding Protein With A Ferroxidase Site.
J. Biol. Inorg. Chem. V. 15 183 2010
PubMed-ID: 19727858  |  Reference-DOI: 10.1007/S00775-009-0582-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DPS-LIKE PEROXIDE RESISTANCE PROTEIN
    Chains: A
    EC Number: 1.16.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: NON-SPECIFIC DNA-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2GOL3Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 36)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL36Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2177 , HOH A:2178 , HOH A:2182BINDING SITE FOR RESIDUE NA A1175
2AC2SOFTWAREHIS A:50 , ASP A:77 , GLU A:81 , GOL A:1177 , HOH A:2065BINDING SITE FOR RESIDUE FE A1176
3AC3SOFTWAREHIS A:50 , HIS A:62 , ASP A:77 , GLU A:81 , LYS A:160 , FE A:1176 , HOH A:2065 , HOH A:2216 , HOH A:2217 , HOH A:2218BINDING SITE FOR RESIDUE GOL A1177
4AC4SOFTWAREARG A:82 , ILE A:86 , LYS A:155 , GLU A:159 , HOH A:2219 , HOH A:2220BINDING SITE FOR RESIDUE GOL A1178
5AC5SOFTWAREALA A:115 , GLN A:116 , ALA A:119 , ARG A:169 , GLN A:171 , HOH A:2203 , HOH A:2205 , HOH A:2221 , HOH A:2222 , HOH A:2223BINDING SITE FOR RESIDUE GOL A1179

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WLU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WLU)

(-) 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:166
 aligned with Q5XAZ8_STRP6 | Q5XAZ8 from UniProtKB/TrEMBL  Length:175

    Alignment length:172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         Q5XAZ8_STRP6     4 TLVENIYASVTHNISKKEASKNEKTKAVLNQAVADLSVAASIVHQVHWYMRGPGFLYLHPKMDELLDSLNANLDEMSERLITIGGAPYSTLAEFSKHSKLDEAKGTYDKTVAQHLARLVEVYLYLSSLYQVGLDITDEEGDAGTNDLFTAAKTEAEKTIWMLQAERGQGPAL 175
               SCOP domains d2wlua_ A: au      tomated matches                                                                                                                                           SCOP domains
               CATH domains 2wluA00 A:4-1      75  [code=1.20.1260.10, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------Ferritin-2wluA01 A:29-172                                                                                                                       --- Pfam domains
         Sec.struct. author hhhhhhhhhhh..------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wlu A   4 TLVENIYASVTHN------SKNEKTKAVLNQAVADLSVAASIVHQVHWYMRGPGFLYLHPKMDELLDSLNANLDEVSERLITIGGAPYSTLAEFSKHSKLDEAKGTYDKTVAQHLARLVEVYLYLSSLYQVGLDITDEEGDAGTNDLFTAAKTEAEKTIWMLQAERGQGPAL 175
                                    13  |     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
                                       16     23                                                                                                                                                        


Chain A from PDB  Type:PROTEIN  Length:166
 aligned with Q99YU7_STRP1 | Q99YU7 from UniProtKB/TrEMBL  Length:175

    Alignment length:172
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
         Q99YU7_STRP1     4 TLVENIYASVTHNISKKEASKNEKTKAVLNQAVADLSVAASIVHQVHWYMRGPGFLYLHPKMDELLDSLNANLDEMSERLITIGGAPYSTLAEFSKHSKLDEAKGTYDKTVAQHLARLVEVYLYLSSLYQVGLDITDEEGDAGTNDLFTAAKTEAEKTIWMLQAERGQGPAL 175
               SCOP domains d2wlua_ A: au      tomated matches                                                                                                                                           SCOP domains
               CATH domains 2wluA00 A:4-1      75  [code=1.20.1260.10, no name defined]                                                                                                                  CATH domains
               Pfam domains -------------------------Ferritin-2wluA01 A:29-172                                                                                                                       --- Pfam domains
         Sec.struct. author hhhhhhhhhhh..------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wlu A   4 TLVENIYASVTHN------SKNEKTKAVLNQAVADLSVAASIVHQVHWYMRGPGFLYLHPKMDELLDSLNANLDEVSERLITIGGAPYSTLAEFSKHSKLDEAKGTYDKTVAQHLARLVEVYLYLSSLYQVGLDITDEEGDAGTNDLFTAAKTEAEKTIWMLQAERGQGPAL 175
                                    13  |     23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173  
                                       16     23
   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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (10, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q99YU7_STRP1 | Q99YU7)
molecular function
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    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:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Chain A   (Q5XAZ8_STRP6 | Q5XAZ8)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0004322    ferroxidase activity    Catalysis of the reaction: 4 Fe2+ + 4 H+ + O2 = 4 Fe3+ + 2 H2O.
    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:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
biological process
    GO:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    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:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

 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 ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ 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 2wlu)
 
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
  2wlu
    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
  Q5XAZ8_STRP6 | Q5XAZ8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q99YU7_STRP1 | Q99YU7
    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)
  1.16.3.1
    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
  Q5XAZ8_STRP6 | Q5XAZ8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q99YU7_STRP1 | Q99YU7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q99YU7_STRP1 | Q99YU7: 2wla 2xgw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2WLU)