Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  UBIQUITIN-LIKE PROTEIN YUKD OF BACILLUS SUBTILIS
 
Authors :  F. Van Den Ent, J. Lowe
Date :  22 Apr 05  (Deposition) - 04 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Yukd, Ubiquitin-Like Protein, Ubiquitin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Van Den Ent, J. Lowe
Crystal Structure Of Ubiquitin-Like Protein Yukd From Bacillus Subtilis
Febs Lett. V. 579 3837 2005
PubMed-ID: 15978580  |  Reference-DOI: 10.1016/J.FEBSLET.2005.06.002

(-) Compounds

Molecule 1 - YUKD PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS17
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2BPS)

(-) Sites  (0, 0)

(no "Site" information available for 2BPS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met A:42 -Pro A:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BPS)

(-) 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:81
 aligned with YUKD_BACSU | P71071 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:81
                              1                                                                              
                              |      8        18        28        38        48        58        68        78 
            YUKD_BACSU    - --MYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL 79
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeeeeee.....hhhhhhhhhhh..........eeee.hhheeee....hhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2bps A -1 HGSYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL 79
                                     8        18        28        38        48        58        68        78 


Chain B from PDB  Type:PROTEIN  Length:81
 aligned with YUKD_BACSU | P71071 from UniProtKB/Swiss-Prot  Length:79

    Alignment length:81
                              1                                                                              
                              |      8        18        28        38        48        58        68        78 
            YUKD_BACSU    - --MYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL 79
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.......eeeeeee.....hhhhhhhhhhh...........eee....eee.....hhhhh.....eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2bps B -1 HGSYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL 79
                                     8        18        28        38        48        58        68        78
   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 2BPS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BPS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BPS)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2BPS)

 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
(no "Ligands, Modified Residues, Ions" information available for 2bps)
 
  Sites
(no "Sites" information available for 2bps)
 
  Cis Peptide Bonds
    Met A:42 - Pro A:43   [ RasMol ]  
 
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 | Biol. Unit 1 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
  2bps
    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
  YUKD_BACSU | P71071
    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
  YUKD_BACSU | P71071
    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 2BPS)

(-) Related Entries Specified in the PDB File

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