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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  SCHIZOSACCHAROMYCES POMBE DJ-1
 
Authors :  M. A. Wilson
Date :  25 Jul 14  (Deposition) - 06 Aug 14  (Release) - 19 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Unknown Function, Cysteine Oxidation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Madzelan, T. Labunska, M. A. Wilson
Influence Of Peptide Dipoles And Hydrogen Bonds On Reactive Cysteine Pk(A) Values In Fission Yeast Dj-1.
Febs J. V. 279 4111 2012
PubMed-ID: 22971103  |  Reference-DOI: 10.1111/FEBS.12004

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN C22E12.03C
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SPAC22E12.03C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896
    Synonym: DJ-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CSD4Mod. Amino Acid3-SULFINOALANINE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3MG5Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1CSD2Mod. Amino Acid3-SULFINOALANINE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:17 , TRP A:21 , SER A:33 , MET A:52 , TYR A:53 , ASN A:55 , VAL B:50 , GLU B:51BINDING SITE FOR RESIDUE EDO A 201
02AC2SOFTWARESER A:63 , ALA A:64 , ASP A:65 , HOH A:356 , HOH A:390BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWARESER A:47 , ARG A:48 , GLY A:79 , GLY A:80 , HOH A:308 , HOH A:474 , HOH A:475 , HOH A:509 , ARG B:26BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWAREHOH B:428 , HOH B:489 , HOH B:490 , HOH B:491BINDING SITE FOR RESIDUE MG B 201
05AC5SOFTWAREPHE C:17 , TRP C:21 , SER C:33 , MET C:52 , TYR C:53 , ASN C:55 , VAL D:50 , GLU D:51BINDING SITE FOR RESIDUE EDO C 201
06AC6SOFTWAREGLU C:14 , PHE C:17 , SER C:18 , MET C:46 , MET C:52 , HOH C:485 , SER D:18 , HOH D:352BINDING SITE FOR RESIDUE EDO C 202
07AC7SOFTWARESER C:47 , ARG C:48 , GLY C:79 , GLY C:80 , HOH C:304 , HOH C:333 , HOH C:459 , HOH C:561 , ARG D:26BINDING SITE FOR RESIDUE EDO C 203
08AC8SOFTWAREHOH C:445 , HOH C:446 , HOH C:470 , HOH C:479 , HOH D:344 , HOH D:350BINDING SITE FOR RESIDUE MG C 204
09AC9SOFTWAREHOH A:457 , HOH C:301 , HOH C:503 , HOH C:504 , HOH C:505BINDING SITE FOR RESIDUE MG C 205
10BC1SOFTWAREHOH B:475 , HOH C:430 , HOH C:487 , HOH C:517BINDING SITE FOR RESIDUE MG C 206
11BC2SOFTWAREVAL C:50 , GLU C:51 , PHE D:17 , TRP D:21 , SER D:33 , TYR D:53 , ASN D:55BINDING SITE FOR RESIDUE EDO D 201
12BC3SOFTWAREGLY C:135 , GLU C:139 , HOH C:343 , CSD D:111 , ALA D:112 , SER D:132BINDING SITE FOR RESIDUE EDO D 202
13BC4SOFTWAREGLU B:139 , HOH B:339 , HOH B:397 , HOH B:398 , GLY D:141 , HOH D:449 , HOH D:450BINDING SITE FOR RESIDUE MG D 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4QYT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QYT)

(-) 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:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh...eeeeee......eee.....eee..ee.hhh.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhh.....ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyt A   2 VKVCLFVADGTDEIEFSAPWGIFKRAEIPIDSVYVGENKDRLVKMSRDVEMYANRSYKEIPSADDFAKQYDIAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIcAGTLTAKTSGLPNKQITGHPSVRGQLEEGGYKYLDQPVVLEENLITSQGPGTAMLFGLKLLEQVASKDKYNAVYKSLSMP 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
                                                                                                                                       111-CSD                                                                            


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh...eeeeee......eee.....eee..ee.hhh.hhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhh.....ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyt B   2 VKVCLFVADGTDEIEFSAPWGIFKRAEIPIDSVYVGENKDRLVKMSRDVEMYANRSYKEIPSADDFAKQYDIAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIcAGTLTAKTSGLPNKQITGHPSVRGQLEEGGYKYLDQPVVLEENLITSQGPGTAMLFGLKLLEQVASKDKYNAVYKSLSMP 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
                                                                                                                                       111-CSD                                                                            


Chain C from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh...eeeeee......eee.....eee..ee.hhh.hhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhh.....ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyt C   2 VKVCLFVADGTDEIEFSAPWGIFKRAEIPIDSVYVGENKDRLVKMSRDVEMYANRSYKEIPSADDFAKQYDIAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIcAGTLTAKTSGLPNKQITGHPSVRGQLEEGGYKYLDQPVVLEENLITSQGPGTAMLFGLKLLEQVASKDKYNAVYKSLSMP 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
                                                                                                                                       111-CSD                                                                            


Chain D from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhh...eeeeee......eee.....eee..ee.hhh.hhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhh.....ee..hhhhhhhhhhh..ee....eeee..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qyt D   2 VKVCLFVADGTDEIEFSAPWGIFKRAEIPIDSVYVGENKDRLVKMSRDVEMYANRSYKEIPSADDFAKQYDIAIIPGGGLGAKTLSTTPFVQQVVKEFYKKPNKWIGMIcAGTLTAKTSGLPNKQITGHPSVRGQLEEGGYKYLDQPVVLEENLITSQGPGTAMLFGLKLLEQVASKDKYNAVYKSLSMP 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
                                                                                                                                       111-CSD
   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 4GDH: 1,4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qyt)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4qyt
    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
  DJ1_SCHPO | Q10356
    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)
  (no 'Enzyme Classificator' available)
    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
  DJ1_SCHPO | Q10356
    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
        DJ1_SCHPO | Q10356: 4ge0 4ge3

(-) Related Entries Specified in the PDB File

4gdh THESE COORDINATES SUPERSEDE THAT ENTRY
4ge0 SCHIZOSACCHAROMYCES POMBE DJ-1 T114P MUTANT
4ge3 SCHIZOSACCHAROMYCES POMBE DJ-1 T114V MUTANT