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(-) Description

Title :  STRUCTURE OF CDK INHIBITOR P19INK4D
 
Authors :  R. Baumgartner, C. Fernandez-Catalan, A. Winoto, R. Huber, R. Engh, T. A. Holak
Date :  12 May 98  (Deposition) - 14 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Tumor Suppressor, Cdk4/6 Inhibitor, Ankyrin Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Baumgartner, C. Fernandez-Catalan, A. Winoto, R. Huber, R. A. Engh, T. A. Holak
Structure Of Human Cyclin-Dependent Kinase Inhibitor P19Ink4D: Comparison To Known Ankyrin-Repeat-Containing Structures And Implications For The Dysfunction Of Tumor Suppressor P16Ink4A.
Structure V. 6 1279 1998
PubMed-ID: 9782052  |  Reference-DOI: 10.1016/S0969-2126(98)00128-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P19INK4D CDK4/6 INHIBITOR
    Cellular LocationCYTOPLASM
    Cell LineBL21
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Cellular LocationCYTOPLASM
    Expression System PlasmidPET-15B
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 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 1BD8)

(-) Sites  (0, 0)

(no "Site" information available for 1BD8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BD8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BD8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BD8)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REP_REGIONPS50297 Ankyrin repeat region circular profile.CDN2D_HUMAN7-158  1A:7-158
2ANK_REPEATPS50088 Ankyrin repeat profile.CDN2D_HUMAN73-105  1A:73-105

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003935991bENSE00001515998chr19:10679631-10679189443CDN2D_HUMAN1-47471A:7-4741
1.2ENST000003935992ENSE00000888297chr19:10678093-10677139955CDN2D_HUMAN48-1661191A:48-162115

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:156
 aligned with CDN2D_HUMAN | P55273 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:156
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156      
          CDN2D_HUMAN     7 RAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGASPNVQDTSGTSPVHDAARTGFLDTLKVLVEHGADVNVPDGTGALPIHLAVQEGHTAVVSFLAAESDLHRRDARGLTPLELALQRGAQDLVDILQGHM 162
               SCOP domains d1bd8a_ A: Cell cycle inhibitor p19ink4D                                                                                                                     SCOP domains
               CATH domains 1bd8A00 A:7-162  [code=1.25.40.20, no name defined]                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhh...............hhhh.....hhhhhhhhhh.............hhhhhhhh..hhhhhhhhh..............hhhhhhhh..hhhhhhhh..............hhhhhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ANK_REP_REGION  PDB: A:7-158 UniProt: 7-158                                                                                                             ---- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------ANK_REPEAT  PDB: A:73-105        --------------------------------------------------------- PROSITE (2)
               Transcript 1 Exon 1.1b  PDB: A:7-47 UniProt: 1-47     Exon 1.2  PDB: A:48-162 UniProt: 48-166 [INCOMPLETE]                                                                Transcript 1
                 1bd8 A   7 RAGDRLSGAAARGDVQEVRRLLHRELVHPDALNRFGKTALQVMMFGSTAIALELLKQGASPNVQDTSGTSPVHDAARTGFLDTLKVLVEHGADVNVPDGTGALPIHLAVQEGHTAVVSFLAAESDLHRRDARGLTPLELALQRGAQDLVDILQGHM 162
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156      

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  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/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BD8)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CDN2D_HUMAN | P55273)
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:0000731    DNA synthesis involved in DNA repair    Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
    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:0048102    autophagic cell death    A form of programmed cell death that is accompanied by the formation of autophagosomes. Autophagic cell death is characterized by lack of chromatin condensation and massive vacuolization of the cytoplasm, with little or no uptake by phagocytic cells.
    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:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:1902230    negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage.
    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: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.
    GO:0009411    response to UV    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0033280    response to vitamin D    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

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        CDN2D_HUMAN | P552731bi8

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