1PF6 - JenaLib

Theoretical Model (Jmol Viewer)

Title :   IN SILICO STRUCTURE OF PROTEIN KINASE 9

Authors :   S. C. Mallena, J. A. R. P. Sarma, M. B. Kanchana, G. Rambabu

Date :   24 May 03 (Deposition) - 03 Jun 03 (Release) - 03 Jun 03 (Revision)

Method :   THEORETICAL MODEL

Resolution :   NOT APPLICABLE

Chains :   Theor. Model : A

Keywords :   Transferase, Serine/Threonine-Protein Kinase, Dr. Mallena, Atp-Binding, Nuclear Protein, Polymorphism, Insight Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Mallena, J. A. R. P. Sarma, M. B. Kanchana, G. Rambabu
In Silico Structrue Of Protein Kinase 9
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CELL DIVISION PROTEIN KINASE 9
	Chains	:	A
	EC Number	:	2.7.1.-
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Synonym	:	SERINE/THREONINE-PROTEIN KINASE PITALRE, C-2K


Theoretical Model	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1PF6)

(no "Site" information available for 1PF6)

(no "SS Bond" information available for 1PF6)

(no "Cis Peptide Bond" information available for 1PF6)

Theoretical Model (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041982	F	59	L	CDK9_HUMAN	Polymorphism	55640715	A	F	59	L
2	UniProt	VAR_013456	G	231	A	CDK9_HUMAN	Polymorphism	---	A	A	231	A

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.	CDK9_HUMAN	25-48	1	A:25-48
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CDK9_HUMAN	145-157	1	A:145-157

Theoretical Model (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000373264	1c	ENSE00001251705	chr9:130548328-130548519	192	CDK9_HUMAN	1-31	31	1	A:1-31	31
1.2a	ENST00000373264	2a	ENSE00000984615	chr9:130548980-130549061	82	CDK9_HUMAN	31-58	28	1	A:31-58	28
1.3c	ENST00000373264	3c	ENSE00000984616	chr9:130549797-130549887	91	CDK9_HUMAN	59-89	31	1	A:59-89	31
1.4	ENST00000373264	4	ENSE00000984617	chr9:130550226-130550392	167	CDK9_HUMAN	89-144	56	1	A:89-144	56
1.5b	ENST00000373264	5b	ENSE00000984618	chr9:130550493-130550664	172	CDK9_HUMAN	145-202	58	1	A:145-202	58
1.6c	ENST00000373264	6c	ENSE00000984619	chr9:130550823-130550971	149	CDK9_HUMAN	202-251	50	1	A:202-251	50
1.7c	ENST00000373264	7c	ENSE00001814236	chr9:130551457-130553066	1610	CDK9_HUMAN	252-372	121	1	A:252-372	121

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:372
 aligned with CDK9_HUMAN | P50750 from UniProtKB/Swiss-Prot  Length:372

    Alignment length:372
                                    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       310       320       330       340       350       360       370  
           CDK9_HUMAN     1 MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHLTSMFEYLAPPRRKGSQITQQSTNQSRNPATTNQTEFERVF 372
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................eee......eeee........eeeeee.........hhhhhhhhhhhhhh.......eeeee.............eeeeee...eehhhhh.......hhhhhhhhhhhhhhhhhhhhhh.ee.........ee.....ee.......ee.................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.........hhhhh..hhhhh.............hhhhhh.......hhhhhhh.......hhhhhhhh............................hhhhhhhhh....hhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: A:1-31         ---------------------------Exon 1.3c  PDB: A:59-89        -------------------------------------------------------Exon 1.5b  PDB: A:145-202 UniProt: 145-202                -------------------------------------------------Exon 1.7c  PDB: A:252-372 UniProt: 252-372                                                                                Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.2a  PDB: A:31-58     ------------------------------Exon 1.4  PDB: A:89-144 UniProt: 89-144                 ---------------------------------------------------------Exon 1.6c  PDB: A:202-251 UniProt: 202-251        ------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1pf6 A   1 MAKQYDSVECPFCDEVSKYEKLAKIGQGTFGEVFKARHRKTGQKVALKKVLMENEKEGFPITALREIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKRVMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTLWYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQANTEQHQLALISQLCGSITPEVWPNVDNYELYEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPMPSDLKGMLSTHLTSMFEYLAPPRRKGSQITQQSTNQSRNPATTNQTEFERVF 372
                                    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       310       320       330       340       350       360       370

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 1PF6)

(no "CATH Domain" information available for 1PF6)

(no "Pfam Domain" information available for 1PF6)

Theoretical Model(hide GO term definitions)

Chain A (CDK9_HUMAN | P50750)

molecular function
	GO:0097322	7SK snRNA binding	Interacting selectively and non-covalently with a 7SK small nuclear RNA (7SK snRNA).
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0008353	RNA polymerase II carboxy-terminal domain kinase activity	Catalysis of the reaction: ATP + (DNA-directed RNA polymerase II) = ADP + phospho-(DNA-directed RNA polymerase II); phosphorylation occurs on residues in the carboxy-terminal domain (CTD) repeats.
	GO:0000979	RNA polymerase II core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery.
	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: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: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: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:0017069	snRNA binding	Interacting selectively and non-covalently with a small nuclear RNA (snRNA).
	GO:0001223	transcription coactivator binding	Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
	GO:0008134	transcription factor binding	Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	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:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	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:0071345	cellular response to cytokine 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 cytokine stimulus.
	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:1900364	negative regulation of mRNA polyadenylation	Any process that stops, prevents or reduces the frequency, rate or extent of mRNA polyadenylation.
	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:0010613	positive regulation of cardiac muscle hypertrophy	Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
	GO:2001168	positive regulation of histone H2B ubiquitination	Any process that activates or increases the frequency, rate or extent of histone H2B ubiquitination.
	GO:0033129	positive regulation of histone phosphorylation	Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.
	GO:1903839	positive regulation of mRNA 3'-UTR binding	Any process that activates or increases the frequency, rate or extent of mRNA 3'-UTR binding.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0050434	positive regulation of viral transcription	Any process that activates or increases the frequency, rate or extent of viral transcription.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0006282	regulation of DNA repair	Any process that modulates the frequency, rate or extent of DNA repair.
	GO:0031056	regulation of histone modification	Any process that modulates the frequency, rate or extent of the covalent alteration of a histone.
	GO:0007346	regulation of mitotic cell cycle	Any process that modulates the rate or extent of progress through the mitotic cell cycle.
	GO:0051147	regulation of muscle cell differentiation	Any process that modulates the frequency, rate or extent of muscle cell differentiation.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0031297	replication fork processing	The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
	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:0042795	snRNA transcription from RNA polymerase II promoter	The synthesis of small nuclear RNA (snRNA) from a DNA template by RNA Polymerase II (Pol II), originating at a Pol II promoter.
	GO:0006368	transcription elongation from RNA polymerase II promoter	The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006367	transcription initiation from RNA polymerase II promoter	Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0016605	PML body	A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
	GO:0008024	cyclin/CDK positive transcription elongation factor complex	A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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:0008023	transcription elongation factor complex	Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.

Theoretical Model
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1fin	CYCLIN A - CYCLIN-DEPENDENT KINASE 2 COMPLEX

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (2, 2)

Exons (7, 7)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (51, 51)

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