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 THE OSK DOMAIN OF DROSOPHILA OSKAR
 
Authors :  M. Jeske, S. Glatt, A. Ephrussi, C. W. Mueller
Date :  05 Jun 15  (Deposition) - 22 Jul 15  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Rna-Binding Protein, Sgnh Hydrolase, Rna Binding, Germ Plasm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jeske, M. Bordi, S. Glatt, S. Muller, V. Rybin, C. W. Muller, A. Ephrussi
The Crystal Structure Of The Drosophila Germline Inducer Oskar Identifies Two Domains With Distinct Vasa Helicase- And Rna-Binding Activities.
Cell Rep. V. 12 587 2015
PubMed-ID: 26190108  |  Reference-DOI: 10.1016/J.CELREP.2015.06.055

(-) Compounds

Molecule 1 - MATERNAL EFFECT PROTEIN OSKAR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: OSK DOMAIN, RESIDUES 401-606
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: OSKAR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:572 , ASN A:589 , LYS A:590 , ARG A:593 , HOH A:2197 , HOH A:2223 , HOH A:2252 , HOH A:2253 , HOH A:2254BINDING SITE FOR RESIDUE SO4 A1607
2AC2SOFTWAREGLN A:572 , ALA A:573 , SER A:574 , ARG A:576 , HOH A:2197 , HOH A:2201 , HOH A:2253BINDING SITE FOR RESIDUE SO4 A1608
3AC3SOFTWAREARG A:490 , SER A:581 , LYS A:582 , GLU A:583 , HOH A:2255BINDING SITE FOR RESIDUE SO4 A1609
4AC4SOFTWAREASN A:406 , SER A:408 , ARG A:444 , ARG A:445 , HIS A:446 , GLU A:447 , HOH A:2064 , HOH A:2065 , HOH A:2256BINDING SITE FOR RESIDUE SO4 A1610
5AC5SOFTWAREARG A:436 , ARG A:442 , PHE A:443 , HOH A:2061 , HOH A:2062 , HOH A:2151 , HOH A:2257BINDING SITE FOR RESIDUE SO4 A1611
6AC6SOFTWAREARG A:465 , HIS A:499 , LEU A:503 , HOH A:2076BINDING SITE FOR RESIDUE SO4 A1612

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A4A)

(-) Exons   (0, 0)

(no "Exon" information available for 5A4A)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.......ee..eeeeehhhhhhhhhhhh...........ee.eee...hhhhhhhhhhh.......eeeee.hhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeee....hhhhh.hhhhhhhhhhhhhhhhhhh....ee..hhhh.......hhhh..................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a4a A 399 GHTSGTYNDSLLTINSDYDAYLLDFPLMGDDFMLYLARMELKCRFRRHERVLQSGLCVSGLTINGARNRLKRVQLPEGTQIIVNIGSVDIMRGKPLVQIEHDFRLLIKEMHNMRLVPILTNLAPLGNYCHDKVLCDKIYRFNKFIRSECCHLKVIDIHSCLINERGVVRFDCFQASPRQVTGSKEPYLFWNKIGRQRVLQVIETSLEY 606
                                   408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598
   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)

(no "SCOP Domain" information available for 5A4A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A4A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A4A)

(-) Gene Ontology  (26, 26)

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
    SO4  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5a4a)
 
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
  5a4a
    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
  OSKA_DROME | P25158
    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
  OSKA_DROME | P25158
    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
        OSKA_DROME | P25158: 5a48 5a49 5cd7 5cd8 5cd9 5nt7

(-) Related Entries Specified in the PDB File

5a48 CRYSTAL STRUCTURE OF THE LOTUS DOMAIN OF DROSOPHILA OSKAR
5a49 CRYSTAL STRUCTURE OF THE LOTUS DOMAIN (AA 139-222) OF DROSOPHILA OSKAR IN C222