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 :  SOLUTION STRUCTURE OF P18-INK4C, 21 STRUCTURES
 
Authors :  I. -J. L. Byeon, J. Li, M. -D. Tsai
Date :  15 Sep 98  (Deposition) - 13 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Cell Cycle Inhibitor, P18Ink4C, Tumor, Suppressor, Cyclin- Dependent Kinase, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Li, I. J. Byeon, K. Ericson, M. J. Poi, P. O'Maille, T. Selby, M. D. Tsai
Tumor Suppressor Ink4: Determination Of The Solution Structure Of P18Ink4C And Demonstration Of The Functional Significance Of Loops In P18Ink4C And P16Ink4A.
Biochemistry V. 38 2930 1999
PubMed-ID: 10074345  |  Reference-DOI: 10.1021/BI982286E
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (CYCLIN-DEPENDENT KINASE 6 INHIBITOR)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidDL21(DE3)
    Expression System StrainDL21(DE3)
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP18-INK4C

 Structural Features

(-) Chains, Units

  
NMR Structure (21x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1BU9)

(-) Sites  (0, 0)

(no "Site" information available for 1BU9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BU9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BU9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_001490A72PCDN2C_HUMANUnclassified  ---AA72P
2UniProtVAR_038604T126MCDN2C_HUMANPolymorphism17851380AT126M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

NMR Structure (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.CDN2C_HUMAN9-161  1A:9-161
2ANK_REPEATPS50088 Ankyrin repeat profile.CDN2C_HUMAN69-101
102-128
  2A:69-101
A:102-128

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003961482bENSE00001524054chr1:51434367-514355711205CDN2C_HUMAN-00--
1.3bENST000003961483bENSE00001064516chr1:51436030-51436169140CDN2C_HUMAN1-43431A:1-4343
1.4bENST000003961484bENSE00001064515chr1:51439565-51440305741CDN2C_HUMAN44-1681251A:44-168125

(-) 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:168
 aligned with CDN2C_HUMAN | P42773 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
          CDN2C_HUMAN     1 MAEPWGNELASAAARGDLEQLTSLLQNNVNVNAQNGFGRTALQVMKLGNPEIARRLLLRGANPDLKDRTGFAVIHDAARAGFLDTLQTLLEFQADVNIEDNEGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTACDLARLYGRNEVVSLMQANGAGGATNLQ 168
               SCOP domains d1bu9a_ A: p18ink4C(ink6)                                                                                                                                                SCOP domains
               CATH domains 1bu9A00 A:1-168  [code=1.25.40.20, no name defined]                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhh..hhhhhhhhh..............hhhh.....hhhhhhhhh..............hhhhhhh...hhhhhhhhh..............hhhhhhh...hhhhhhhh................hhhhhhhh..hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------P-----------------------------------------------------M------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------ANK_REP_REGION  PDB: A:9-161 UniProt: 9-161                                                                                                              ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------ANK_REPEAT  PDB: A:69-101        ANK_REPEAT  PDB: A:102-128 ---------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.3b  PDB: A:1-43 UniProt: 1-43       Exon 1.4b  PDB: A:44-168 UniProt: 44-168                                                                                      Transcript 1
                 1bu9 A   1 MAEPWGNELASAAARGDLEQLTSLLQNNVNVNAQNGFGRTALQVMKLGNPEIARRLLLRGANPDLKDRTGFAVIHDAARAGFLDTLQTLLEFQADVNIEDNEGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTACDLARLYGRNEVVSLMQANGAGGATNLQ 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        

   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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BU9)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (CDN2C_HUMAN | P42773)
molecular function
    GO:0004861    cyclin-dependent protein serine/threonine kinase inhibitor activity    Stops, prevents or reduces the activity of a cyclin-dependent protein serine/threonine kinase.
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0030308    negative regulation of cell growth    Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0042326    negative regulation of phosphorylation    Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule.
    GO:0071901    negative regulation of protein serine/threonine kinase activity    Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0048709    oligodendrocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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 1bu9)
 
  Sites
(no "Sites" information available for 1bu9)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1bu9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1bu9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CDN2C_HUMAN | P42773
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CDN2C_HUMAN | P42773
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CDN2C_HUMAN | P427731g3n 1ihb 1mx2 1mx4 1mx6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BU9)