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
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THERMOSYNECHOCOCCUS ELONGATUS BP-1 KAIA
 
Authors :  T. Uzumaki, M. Fujita, T. Nakatsu, F. Hayashi, H. Shibata, N. Itoh, H. Ka M. Ishiura, Riken Structural Genomics/Proteomics Initiative (
Date :  20 Oct 03  (Deposition) - 01 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  All Alpha, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Circadian Clock Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Uzumaki, M. Fujita, T. Nakatsu, F. Hayashi, H. Shibata, N. Itoh, H. Kato, M. Ishiura
Crystal Structure Of The C-Terminal Clock-Oscillator Domain Of The Cyanobacterial Kaia Protein
Nat. Struct. Mol. Biol. V. 11 623 2004
PubMed-ID: 15170179  |  Reference-DOI: 10.1038/NSMB781

(-) Compounds

Molecule 1 - CIRCADIAN CLOCK PROTEIN KAIA HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Strain: BP-1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1V2Z)

(-) Sites  (0, 0)

(no "Site" information available for 1V2Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V2Z)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KAIA_CPS51431 KaiA C-terminal domain profile.KAIA_THEEB173-281  1A:174-278
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KAIA_CPS51431 KaiA C-terminal domain profile.KAIA_THEEB173-281  2A:174-278

(-) Exons   (0, 0)

(no "Exon" information available for 1V2Z)

(-) 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:106
 aligned with KAIA_THEEB | Q79V62 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:106
                                   182       192       202       212       222       232       242       252       262       272      
           KAIA_THEEB   173 DTAFFFRRMSPADKRKLLDELRSIYRTIVLEYFNTDAKVNERIDEFVSKAFFADISVSQVLEIHVELMDTFSKQLKLEGRSEDILLDYRLTLIDVIAHLCEMYRRS 278
               SCOP domains d1v2za_ A: Circadian clock protein KaiA, C-terminal domain                                                 SCOP domains
               CATH domains 1v2zA00 A:173-278 KaiA/RbsU domain                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE KAIA_C  PDB: A:174-278 UniProt: 173-281                                                                    PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1v2z A 173 STAFFFRRMSPADKRKLLDELRSIYRTIVLEYFNTDAKVNERIDEFVSKAFFADISVSQVLEIHVELMDTFSKQLKLEGRSEDILLDYRLTLIDVIAHLCEMYRRS 278
                                   182       192       202       212       222       232       242       252       262       272
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V2Z)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (KAIA_THEEB | Q79V62)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.

 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 1v2z)
 
  Sites
(no "Sites" information available for 1v2z)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1v2z)
 
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 | Biol. Unit 1 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
  1v2z
    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
  KAIA_THEEB | Q79V62
    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
  KAIA_THEEB | Q79V62
    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
        KAIA_THEEB | Q79V62: 1q6a 1q6b 1suy 1sv1 5jwr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1V2Z)