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 :  CRYSTAL STRUCTURE OF HUMAN C53A DJ-1
 
Authors :  L. Cendron, S. Girotto, M. Bisaglia, I. Tessari, S. Mammi, G. Zanotti, L
Date :  19 Sep 13  (Deposition) - 05 Mar 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Homodimer, Rossmann Fold, Alpha/Beta Protein, Chaperone, Oxidative Stress Protection, Cytosol, Mitochondrion, Nucleus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Girotto, L. Cendron, M. Bisaglia, I. Tessari, S. Mammi, G. Zanotti, L. Bubacco
Dj-1 Is A Copper Chaperone Acting On Sod1 Activation.
J. Biol. Chem. V. 289 10887 2014
PubMed-ID: 24567322  |  Reference-DOI: 10.1074/JBC.M113.535112

(-) Compounds

Molecule 1 - PROTEIN DJ-1
    ChainsA
    EC Number3.4.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePARK7
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymONCOGENE DJ1, PARKINSON DISEASE PROTEIN 7

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:28 , HIS A:126 , PRO A:184 , HOH A:435 , HOH A:473BINDING SITE FOR RESIDUE EDO A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:65 -Pro A:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MTC)

(-) 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:187
                                                                                                                                                                                                                           
               SCOP domains d4mtca_ A: DJ-1                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhh..eeeeee......ee.....ee...eehhhhh......eeee..hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhh......ee..hhhhhhhhh.....ee....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mtc A   2 ASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVIAPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLK 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (136, 136)

Asymmetric Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:65 - Pro A:66   [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4mtc
    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
  PARK7_HUMAN | Q99497
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.-.-
    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
  PARK7_HUMAN | Q99497
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PARK7_HUMAN | Q994971j42 1p5f 1pdv 1pdw 1pe0 1q2u 1soa 1ucf 2or3 2r1t 2r1u 2r1v 2rk3 2rk4 2rk6 3b36 3b38 3b3a 3bwe 3cy6 3cyf 3cz9 3cza 3ezg 3f71 3sf8 4bte 4mnt 4n0m 4n12 4ogf 4oq4 4p2g 4p34 4p35 4p36 4rkw 4rky 4s0z 4zgg 5ip5 5sy6 5sy9 5sya

(-) Related Entries Specified in the PDB File

4mnt CRYSTAL STRUCTURE OF HUMAN DJ-1 IN COMPLEX WITH CU