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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL STRUCTURE OF HUMAN-CYCLIN DEPENDENT KINASE 3 (CDK3)
 
Authors :  K. Narayana, T. Rajasekhar, J. A. R. P. Sarma
Date :  11 Apr 02  (Deposition) - 24 Apr 02  (Release) - 24 Apr 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Transferase, Serine/Threonine-Protein Kinase, Atp-Binding, Cell Cycle, Cell Division, Mitosis, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Narayana, T. Rajasekhar, J. A. R. P. Sarma
Theoretical Structure Of Human Cyclin-Dependent Kinase 3 (Cdk3)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELL DIVISION PROTEIN KINASE 3
    ChainsA
    EC Number2.7.1.-
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCYCLIN-DEPENDENT KINASE 3, CDK3

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1LFN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Theoretical Model (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041973S106NCDK3_HUMANUnclassified  ---AS106N
2UniProtVAR_041974I124TCDK3_HUMANPolymorphism34918446AI124T
3UniProtVAR_041975R214HCDK3_HUMANPolymorphism34670267AR214H
4UniProtVAR_021101T226ICDK3_HUMANPolymorphism2069532AT226I
5UniProtVAR_021102M264TCDK3_HUMANPolymorphism17884251AM264T

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

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.CDK3_HUMAN10-33  1A:10-33
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.CDK3_HUMAN123-135  1A:123-135

(-) Exons   (0, 0)

(no "Exon" information available for 1LFN)

(-) Sequences/Alignments

Theoretical Model
   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:305
 aligned with CDK3_HUMAN | Q00526 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     
           CDK3_HUMAN     1 MDMFQKVEKIGEGTYGVVYKAKNRETGQLVALKKIRLDLEMEGVPSTAIREISLLKELKHPNIVRLLDVVHNERKLYLVFEFLSQDLKKYMDSTPGSELPLHLIKSYLFQLLQGVSFCHSHRVIHRDLKPQNLLINELGAIKLADFGLARAFGVPLRTYTHEVVTLWYRAPEILLGSKFYTTAVDIWSIGCIFAEMVTRKALFPGDSEIDQLFRIFRMLGTPSEDTWPGVTQLPDYKGSFPKWTRKGLEEIVPNLEPEGRDLLMQLLQYDPSQRITAKTALAHPYFSSPEPSPAARQYVLQRFRH 305
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....eeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..ee..............hhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------N-----------------T-----------------------------------------------------------------------------------------H-----------I-------------------------------------T----------------------------------------- SAPs(SNPs)
                    PROSITE ---------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lfn A   1 MDMFQKVEKIGEGTYGVVYKAKNRETGQLVALKKIRLDLEMEGVPSTAIREISLLKELKHPNIVRLLDVVHNERKLYLVFEFLSQDLKKYMDSTPGSELPLHLIKSYLFQLLQGVSFCHSHRVIHRDLKPQNLLINELGAIKLADFGLARAFGVPLRTYTHEVVTLWYRAPEILLGSKFYTTAVDIWSIGCIFAEMVTRKALFPGDSEIDQLFRIFRMLGTPSEDTWPGVTQLPDYKGSFPKWTRKGLEEIVPNLEPEGRDLLMQLLQYDPSQRITAKTALAHPYFSSPEPSPAARQYVLQRFRH 305
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300     

   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 1LFN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1LFN)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Theoretical Model(hide GO term definitions)
Chain A   (CDK3_HUMAN | Q00526)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004693    cyclin-dependent protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate. This reaction requires the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0045023    G0 to G1 transition    The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression.
    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: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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1dm2 1DM2 CHAIN A HAS 76% SEQUENCE SIMILARITY (E-132) WITH CDK3
1f5q 1F5Q CHAIN A HAS 76% SEQUENCE SIMILARITY (E-132) WITH CDK3
1qmz 1QMZ CHAIN A HAS 76% SEQUENCE SIMILARITY (E-131) WITH CDK3