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Theoretical Model (Jmol Viewer)

Title :   THEORETICAL STRUCTURE OF HUMAN CYCLIN-DEPENDENT KINASE 4 (CDK4)

Authors :   K. Narayana, R. P. K. Surendra, J. A. R. P. Sarma

Date :   08 Apr 02 (Deposition) - 17 Apr 02 (Release) - 17 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, Nuclear Protein, Phosphorylation, Proto-Oncogene (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Narayana, R. P. K. Surendra, J. A. R. P. Sarma
Theoretical Structure Of Human Cyclin-Dependent Kinase 4 (Cdk4)
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CYCLIN-DEPENDENT KINASE 4
	Cellular Location	:	NUCLEUS
	Chains	:	A
	EC Number	:	2.7.1.-
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	(CDK4), CELL DIVISION PROTEIN KINASE 4


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1LD2)

(no "Site" information available for 1LD2)

(no "SS Bond" information available for 1LD2)

(no "Cis Peptide Bond" information available for 1LD2)

Theoretical Model (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_006200	R	24	C	CDK4_HUMAN	Disease (CMM3)	11547328	A	R	24	C
2	UniProt	VAR_006201	R	24	H	CDK4_HUMAN	Disease (CMM3)	104894340	A	R	24	H
3	UniProt	VAR_021152	N	41	S	CDK4_HUMAN	Disease (CMM3)	144890720	A	N	41	S
4	UniProt	VAR_029153	R	82	Q	CDK4_HUMAN	Polymorphism	3211612	A	R	82	Q
5	UniProt	VAR_041976	R	122	H	CDK4_HUMAN	Polymorphism	34386532	A	R	122	H

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

Theoretical Model (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	CDK4_HUMAN	12-35	1	A:12-35
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CDK4_HUMAN	136-148	1	A:136-148

Theoretical Model (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000257904	1a	ENSE00001354290	chr12:58146164-58145958	207	CDK4_HUMAN	-	0	0	-	-
1.2	ENST00000257904	2	ENSE00001386813	chr12:58145519-58145283	237	CDK4_HUMAN	1-73	73	1	A:1-73	73
1.3b	ENST00000257904	3b	ENSE00000920441	chr12:58145125-58144990	136	CDK4_HUMAN	73-118	46	1	A:73-118	46
1.4	ENST00000257904	4	ENSE00000920442	chr12:58144873-58144706	168	CDK4_HUMAN	119-174	56	1	A:119-174	56
1.5a	ENST00000257904	5a	ENSE00001651755	chr12:58144548-58144439	110	CDK4_HUMAN	175-211	37	1	A:175-211	37
1.6	ENST00000257904	6	ENSE00001796462	chr12:58143287-58143237	51	CDK4_HUMAN	211-228	18	1	A:211-228	18
1.7	ENST00000257904	7	ENSE00001635558	chr12:58143100-58142965	136	CDK4_HUMAN	228-273	46	1	A:228-273	46
1.8b	ENST00000257904	8b	ENSE00001141069	chr12:58142400-58142005	396	CDK4_HUMAN	274-303	30	1	A:274-303	30

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:303
 aligned with CDK4_HUMAN | P11802 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:303
                                    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   
           CDK4_HUMAN     1 MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYLHKDEGNPE 303
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeee..eeeeeeee....eeeeeeeeeee.........hhhhhhhhhhhhhhhhhh......eeeeeeee....eeeeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.......eee......eee.hhhh.hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhh......hhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhh........... Sec.struct. author
             SAPs(SNPs) (1) -----------------------C----------------S----------------------------------------Q---------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------H--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:1-73 UniProt: 1-73                                      ---------------------------------------------Exon 1.4  PDB: A:119-174 UniProt: 119-174               Exon 1.5a  PDB: A:175-211            ----------------Exon 1.7  PDB: A:228-273 UniProt: 228-273     Exon 1.8b  PDB: A:274-303      Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.3b  PDB: A:73-118 UniProt: 73-118      --------------------------------------------------------------------------------------------Exon 1.6          --------------------------------------------------------------------------- Transcript 1 (2)
                 1ld2 A   1 MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYLHKDEGNPE 303
                                    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)
	-	→ 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 '\|'

(no "SCOP Domain" information available for 1LD2)

(no "CATH Domain" information available for 1LD2)

(no "Pfam Domain" information available for 1LD2)

Theoretical Model(hide GO term definitions)

Chain A (CDK4_HUMAN | P11802)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0030332	cyclin binding	Interacting selectively and non-covalently with cyclins, proteins whose levels in a cell varies markedly during the cell cycle, rising steadily until mitosis, then falling abruptly to zero. As cyclins reach a threshold level, they are thought to drive cells into G2 phase and thus to mitosis.
	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:0016538	cyclin-dependent protein serine/threonine kinase regulator activity	Modulates the activity of a cyclin-dependent protein serine/threonine kinase, enzymes of the protein kinase family that are regulated through association with cyclins and other proteins.
	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: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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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: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:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	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:0007623	circadian rhythm	Any biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0002088	lens development in camera-type eye	The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus.
	GO:0071157	negative regulation of cell cycle arrest	Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
	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:0010971	positive regulation of G2/M transition of mitotic cell cycle	Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0045787	positive regulation of cell cycle	Any process that activates or increases the rate or extent of progression through the cell cycle.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0045793	positive regulation of cell size	Any process that increases cell size.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:0045727	positive regulation of translation	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	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.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0045859	regulation of protein kinase activity	Any process that modulates the frequency, rate or extent of protein kinase activity.
	GO:0042493	response to drug	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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0055093	response to hyperoxia	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 stimulus indicating increased oxygen tension.
	GO:0010288	response to lead ion	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 lead ion stimulus.
	GO:0010033	response to organic substance	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 organic substance stimulus.
	GO:0033574	response to testosterone	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 testosterone stimulus.
	GO:0009636	response to toxic substance	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 toxic stimulus.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0000307	cyclin-dependent protein kinase holoenzyme complex	Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0005667	transcription factor complex	A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Theoretical Model
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	CDK4_HUMAN \| P11802	:	2w96 2w99 2w9f 2w9z 3g33 5fwk 5fwl 5fwm 5fwp

1g3n	1G3N CHAIN A HAS 68% SEQUENCE SIMILARITY (E-113) WITH CDK4

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Ligands, Modified Residues, Ions (0, 0)

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Exons (7, 7)

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