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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURAL AND THERMODYNAMIC CHARACTERIZATION OF THE TYK2 AND JAK3 KINASE DOMAINS IN COMPLEX WITH CP-690550 AND CMP-6

Authors :   J. E. Chrencik, T. E. Benson

Date :   25 Feb 10 (Deposition) - 02 Jun 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym./Biol. Unit : A

Keywords :   Tyk2, Jak3, Inflammation, Cancer, Pan Inhibitor, Atp-Binding, Disease Mutation, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Scid, Sh2 Domain, Transferase, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Chrencik, A. Patny, I. K. Leung, B. Korniski, T. L. Emmons, T. Hall R. A. Weinberg, J. A. Gormley, J. M. Williams, J. E. Day, J. L. Hirsch, J. R. Kiefer, J. W. Leone, H. D. Fischer, C. D. Sommers, H. C. Huang, E. J. Jacobsen, R. E. Tenbrink, A. G. Tomasselli, T. E. Benson
Structural And Thermodynamic Characterization Of The Tyk2 And Jak3 Kinase Domains In Complex With Cp-690550 And Cmp-6
J. Mol. Biol. V. 400 413 2010
PubMed-ID: 20478313 | Reference-DOI: 10.1016/J.JMB.2010.05.020

Molecule 1 - TYROSINE-PROTEIN KINASE JAK3
	Chains	:	A
	EC Number	:	2.7.10.2
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Plasmid	:	PDEST9
	Expression System Strain	:	SF21
	Expression System Taxid	:	7108
	Expression System Vector Type	:	PLASMID
	Fragment	:	KINASE DOMAIN
	Gene	:	JAK3
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JANUS KINASE 3, JAK-3, LEUKOCYTE JANUS KINASE, L-JAK

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	IZA	1	Ligand/Ion	2-TERT-BUTYL-9-FLUORO-3,6-DIHYDRO-7H-BENZ[H]-IMIDAZ[4,5-F]ISOQUINOLINE-7-ONE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2 , HOH A:273 , LEU A:828 , LYS A:830 , VAL A:836 , ALA A:853 , HIS A:859 , GLU A:903 , TYR A:904 , LEU A:905 , GLY A:908 , ASN A:954 , LEU A:956	BINDING SITE FOR RESIDUE IZA A 1

(no "SS Bond" information available for 3LXL)

(no "Cis Peptide Bond" information available for 3LXL)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_010498	L	910	S	JAK3_HUMAN	Disease (T(-)	---	A	L	910	S

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	JAK3_HUMAN	828-855	1	A:828-855
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	JAK3_HUMAN	945-957	1	A:945-957

(no "Exon" information available for 3LXL)

Asymmetric/Biological Unit

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:281
 aligned with JAK3_HUMAN | P52333 from UniProtKB/Swiss-Prot  Length:1124

    Alignment length:285
                                   823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093     
          JAK3_HUMAN    814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDML 1098
               SCOP domains d3lxla_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Pkinase_Tyr-3lxlA01 A:822-1095                                                                                                                                                                                                                                                    --- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee........eeeeeeee...hhhhhhhhhhhhhhhhh........eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee.hhhhhee......eee.......hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.----.hhhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP          -----------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lxl A  814 PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMG----VPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDML 1098
                                   823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033     |   -|     1053      1063      1073      1083      1093     
                                                                                                                                                                                                                                                          1039 1044

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: automated matches (529)

Protein domain: automated matches (529)

Human (Homo sapiens) [TaxId: 9606] (438)

d3lxla_

(no "CATH Domain" information available for 3LXL)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase_Tyr (229)

Homo sapiens (Human) (202)

Pkinase_Tyr-3lxlA01

A:822-1095

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (JAK3_HUMAN | P52333)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	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:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	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:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0060397	JAK-STAT cascade involved in growth hormone signaling pathway	The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007262	STAT protein import into nucleus	The directed movement of dimerized STAT (Signal Transducers and Activators of Transcription) proteins into the nucleus following activation by members of the janus activated kinase (JAK) family of tyrosine kinases.
	GO:0043029	T cell homeostasis	The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus.
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0019221	cytokine-mediated signaling pathway	A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0007167	enzyme linked receptor protein signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0035771	interleukin-4-mediated signaling pathway	A series of molecular signals initiated by the binding of interleukin-4 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0045221	negative regulation of FasL biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of FasL.
	GO:0050868	negative regulation of T cell activation	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation.
	GO:0045626	negative regulation of T-helper 1 cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation.
	GO:0002731	negative regulation of dendritic cell cytokine production	Any process that stops, prevents, or reduces the frequency, rate, or extent of dendritic cell cytokine production.
	GO:0032693	negative regulation of interleukin-10 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production.
	GO:0032695	negative regulation of interleukin-12 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-12 production.
	GO:0070244	negative regulation of thymocyte apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of thymocyte death by apoptotic process.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0042104	positive regulation of activated T cell proliferation	Any process that activates or increases the rate or extent of activated T cell proliferation.
	GO:0051928	positive regulation of calcium ion transport	Any process that activates or increases the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007204	positive regulation of cytosolic calcium ion concentration	Any process that increases the concentration of calcium ions in the cytosol.
	GO:0050778	positive regulation of immune response	Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
	GO:0046777	protein autophosphorylation	The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0070232	regulation of T cell apoptotic process	Any process that modulates the occurrence or rate of T cell death by apoptotic process.
	GO:0070672	response to interleukin-15	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 interleukin-15 stimulus.
	GO:0070669	response to interleukin-2	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 interleukin-2 stimulus.
	GO:0070670	response to interleukin-4	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 interleukin-4 stimulus.
	GO:0071104	response to interleukin-9	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 interleukin-9 stimulus.
	GO:0007260	tyrosine phosphorylation of STAT protein	The process of introducing a phosphate group to a tyrosine residue of a STAT (Signal Transducer and Activator of Transcription) protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 3lxl)

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	3lxl
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	JAK3_HUMAN \| P52333
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	2.7.10.2
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	600802
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (54, 54)

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