Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  X-RAY STRUCTURE OF A VIRAL CYCLIN FROM HERPESVIRUS SAIMIRI
 
Authors :  U. Schulze-Gahmen, J. U. Jung, S. -H. Kim
Date :  10 Sep 98  (Deposition) - 15 Jun 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Cell Cycle Regulation, Herpesvirus Saimiri, Viral Cyclin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Schulze-Gahmen, J. U. Jung, S. H. Kim
Crystal Structure Of A Viral Cyclin, A Positive Regulator Of Cyclin-Dependent Kinase 6.
Structure Fold. Des. V. 7 245 1999
PubMed-ID: 10368294  |  Reference-DOI: 10.1016/S0969-2126(99)80035-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYCLIN HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE9
    Expression System Strain: DH5ALPHADE3 PACYC
    Expression System Taxid: 562
    Gene: ECLF2
    Organism Scientific: HERPESVIRUS SAIMIRI (STRAIN 11)
    Organism Taxid: 10383
    Strain: 11

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BU2)

(-) Sites  (0, 0)

(no "Site" information available for 1BU2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BU2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BU2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BU2)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYCLINSPS00292 Cyclins signature.CGH2_SHV2152-83  1A:52-83

(-) Exons   (0, 0)

(no "Exon" information available for 1BU2)

(-) Sequences/Alignments

Asymmetric/Biological 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:229
 aligned with CGH2_SHV21 | Q01043 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:229
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
           CGH2_SHV21    22 RVLNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFSLYD 250
               SCOP domains d1bu2a1 A:22-148 Viral cyclin                                                                                                  d1bu2a2 A:149-250 Viral cyclin                                                                         SCOP domains
               CATH domains ---------------1bu2A01 A:37-148  [code=1.10.472.10, no name defined]                                                           1bu2A02 A:149-250  [code=1.10.472.10, no name defined]                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.......hhhhhh.......hhhhhhhhhhhhhh.........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhh..hhhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------CYCLINS  PDB: A:52-83           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bu2 A  22 RVLNNLKLRELLLPKFTSLWEIQTEVTVDNRTILLTWMHLLCESFELDKSVFPLSVSILDRYLCKKQGTKKTLQKIGAACVLIGSKIRTVKPMTVSKLTYLSCDCFTNLELINQEKDILEALKWDTEAVLATDFLIPLCNALKIPEDLWPQLYEAASTTICKALIQPNIALLSPGLICAGGLLTTIETDNTNCRPWTCYLEDLSSILNFSTNTVRTVKDQVSEAFSLYD 250
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BU2)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CGH2_SHV21 | Q01043)
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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 1bu2)
 
  Sites
(no "Sites" information available for 1bu2)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1bu2)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  1bu2
    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
  CGH2_SHV21 | Q01043
    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
  CGH2_SHV21 | Q01043
    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
        CGH2_SHV21 | Q01043: 1jow 1xo2 2euf 2f2c 4tth

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BU2)