Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1
 
Authors :  J. Iwahara, T. Kigawa, K. Kitagawa, H. Masumoto, T. Okazaki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Sep 98  (Deposition) - 07 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Centromere Protein, Dna-Binding, Helix-Turn-Helix, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Iwahara, T. Kigawa, K. Kitagawa, H. Masumoto, T. Okazaki, S. Yokoyama
A Helix-Turn-Helix Structure Unit In Human Centromere Protein B (Cenp-B).
Embo J. V. 17 827 1998
PubMed-ID: 9451007  |  Reference-DOI: 10.1093/EMBOJ/17.3.827
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CENTROMERE PROTEIN B)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHR1
    Expression System Strain: BL21(DE3)/PLYSS
    Expression System Taxid: 562
    Expression System Vector: PRSETA
    Fragment: DNA-BINDING DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BW6)

(-) Sites  (0, 0)

(no "Site" information available for 1BW6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BW6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BW6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BW6)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_PSQPS50960 Psq-type HTH domain profile.CENPB_HUMAN1-52  1A:1-52

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003797511ENSE00001482363chr20:3767337-37645002838CENPB_HUMAN1-6686681A:1-5656

(-) Sequences/Alignments

NMR Structure
   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:56
 aligned with CENPB_HUMAN | P07199 from UniProtKB/Swiss-Prot  Length:599

    Alignment length:56
                                    10        20        30        40        50      
           CENPB_HUMAN    1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASE 56
               SCOP domains d1bw6a_ A:                                               SCOP domains
               CATH domains 1bw6A00 A:1-56 Homeodomain-like                          CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh....hhhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_PSQ  PDB: A:1-52 UniProt: 1-52                  ---- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-56 UniProt: 1-668 [INCOMPLETE]        Transcript 1
                  1bw6 A  1 MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASE 56
                                    10        20        30        40        50
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BW6)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (CENPB_HUMAN | P07199)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0019237    centromeric DNA binding    Interacting selectively and non-covalently with a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003696    satellite DNA binding    Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

NMR Structure
  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 1bw6)
 
  Sites
(no "Sites" information available for 1bw6)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1bw6)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  1bw6
    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
  CENPB_HUMAN | P07199
    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
  CENPB_HUMAN | P07199
    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
        CENPB_HUMAN | P07199: 1hlv 1ufi

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BW6)