3BQR - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN DEATH ASSOCIATED PROTEIN KINASE 3 (DAPK3) IN COMPLEX WITH AN IMIDAZO-PYRIDAZINE LIGAND

Authors :   P. Filippakopoulos, P. Rellos, O. Fedorov, F. Niesen, A. C. W. Pike, E. S F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, S. Knapp, St Genomics Consortium (Sgc)

Date :   20 Dec 07 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Death Associated Kinase, Dapk3, Zip Kinase, Zipk, Dap Kinase 3, Dap Like Kinase, Dlk, Structural Genomics Consortium, Sgc, Apoptosis, Atp-Binding, Chromatin Regulator, Nucleotide-Binding, Nucleus, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, P. Rellos, O. Fedorov, F. Niesen, A. C. W. Pike, E. S. Pilka, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, S. Knapp
Crystal Structure Of Human Death Associated Protein Kinase (Dapk3) In Complex With An Imidazo-Pyridazine Ligand.
To Be Published
PubMed: search

Molecule 1 - DEATH-ASSOCIATED PROTEIN KINASE 3
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)(R3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DAPK3, ZIPK
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DAP KINASE 3, DAP-LIKE KINASE, DLK, ZIP-KINASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	4RB	1	Ligand/Ion	4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZOIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	PGO	2	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	4RB	2	Ligand/Ion	4-(6-{[(1R)-1-(HYDROXYMETHYL)PROPYL]AMINO}IMIDAZO[1,2-B]PYRIDAZIN-3-YL)BENZOIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	PGO	4	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:20 , ALA A:40 , LYS A:42 , GLU A:94 , LEU A:95 , GLU A:100 , MET A:146 , ILE A:160 , ASP A:161 , HOH A:588 , HOH A:632 , HOH A:637 , HOH A:656	BINDING SITE FOR RESIDUE 4RB A 401
2	AC2	SOFTWARE	ARG A:69 , ASP A:81	BINDING SITE FOR RESIDUE PGO A 501
3	AC3	SOFTWARE	TYR A:234 , PHE A:236 , ARG A:253	BINDING SITE FOR RESIDUE PGO A 502
4	AC4	SOFTWARE	LYS A:42 , ILE A:44 , GLU A:64 , ASP A:161 , HOH A:689 , HOH A:779	BINDING SITE FOR RESIDUE GOL A 503

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

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

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040438	T	112	M	DAPK3_HUMAN	Unclassified	---	A	T	112	M
2	UniProt	VAR_040439	D	161	N	DAPK3_HUMAN	Unclassified	---	A	D	161	N
3	UniProt	VAR_040440	P	216	S	DAPK3_HUMAN	Unclassified	---	A	P	216	S

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

Biological Unit 1 (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040438	T	112	M	DAPK3_HUMAN	Unclassified	---	A	T	112	M
2	UniProt	VAR_040439	D	161	N	DAPK3_HUMAN	Unclassified	---	A	D	161	N
3	UniProt	VAR_040440	P	216	S	DAPK3_HUMAN	Unclassified	---	A	P	216	S

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

Asymmetric 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.	DAPK3_HUMAN	19-46	1	A:19-46
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	DAPK3_HUMAN	135-147	1	A:135-147

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	DAPK3_HUMAN	19-46	2	A:19-46
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	DAPK3_HUMAN	135-147	2	A:135-147

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000301264	1	ENSE00002166557	chr19:3969826-3969672	155	DAPK3_HUMAN	1-21	21	1	A:7-21	15
1.2	ENST00000301264	2	ENSE00001643526	chr19:3964989-3964629	361	DAPK3_HUMAN	21-141	121	1	A:21-141	121
1.3	ENST00000301264	3	ENSE00001806720	chr19:3964371-3964242	130	DAPK3_HUMAN	142-185	44	1	A:142-185 (gaps)	44
1.4	ENST00000301264	4	ENSE00001115355	chr19:3963917-3963869	49	DAPK3_HUMAN	185-201	17	1	A:185-201	17
1.5	ENST00000301264	5	ENSE00001115354	chr19:3963667-3963641	27	DAPK3_HUMAN	201-210	10	1	A:201-210	10
1.6	ENST00000301264	6	ENSE00001115351	chr19:3961159-3961007	153	DAPK3_HUMAN	210-261	52	1	A:210-261	52
1.7	ENST00000301264	7	ENSE00001115349	chr19:3960102-3960057	46	DAPK3_HUMAN	261-276	16	1	A:261-276	16
1.8b	ENST00000301264	8b	ENSE00001267404	chr19:3959635-3958452	1184	DAPK3_HUMAN	277-454	178	1	A:277-284	8

Asymmetric 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:275
 aligned with DAPK3_HUMAN | O43293 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:278
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276        
          DAPK3_HUMAN     7 EDVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAIRRRNVR 284
               SCOP domains d3bqra_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------3bqrA02 A:99-284 Transferase(Phosphotransferase) domain 1                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeeeeeee...eeeeeeee.....eeeeeeee...........hhhhhhhhhhhhhhh.......eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.........eee......ee.....---.........hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------M------------------------------------------------N------------------------------------------------------S-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP          ----------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1       ------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:142-185 (gaps)             ---------------Exon 1.5  --------------------------------------------------Exon 1.7        1.8b     Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2  PDB: A:21-141 UniProt: 21-141                                                                                  -------------------------------------------Exon 1.4         --------Exon 1.6  PDB: A:210-261 UniProt: 210-261           ----------------------- Transcript 1 (2)
                 3bqr A   7 SMVEDHYEMGEELGSGQFAIVRKCRQKGTGKEYAAKFIKKRRLSSSRRGVSREEIEREVNILREIRHPNIITLHDIFENKTDVVLILELVSGGELFDFLAEKESLTEDEATQFLKQILDGVHYLHSKRIAHFDLKPENIMLLDKNVPNPRIKLIDFGIAHKIEAGN---NIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGETKQETLTNISAVNYDFDEEYFSNTSELAKDFIRRLLVKDPKRRMTIAQSLEHSWIKAIRRRNVR 284
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166     | 176       186       196       206       216       226       236       246       256       266       276        
                                                                                                                                                                                               172 176

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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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

d3bqra_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

3bqrA02

A:99-284

(no "Pfam Domain" information available for 3BQR)

Asymmetric Unit(hide GO term definitions)

Chain A (DAPK3_HUMAN | O43293)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0017048	Rho GTPase binding	Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
	GO:0008140	cAMP response element binding protein binding	Interacting selectively and non-covalently with a cAMP response element binding protein (a CREB protein).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0043522	leucine zipper domain binding	Interacting selectively and non-covalently with a leucine zipper domain, a protein secondary structure exhibiting a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns.
	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:0008022	protein C-terminus binding	Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0071346	cellular response to interferon-gamma	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 an interferon-gamma stimulus. Interferon gamma is the only member of the type II interferon found so far.
	GO:0000910	cytokinesis	The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
	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:0017148	negative regulation of translation	Any process that stops, prevents, or reduces 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:0030182	neuron differentiation	The process in which a relatively unspecialized cell acquires specialized features of a neuron.
	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:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0090263	positive regulation of canonical Wnt signaling pathway	Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:2001241	positive regulation of extrinsic apoptotic signaling pathway in absence of ligand	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
	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:2000249	regulation of actin cytoskeleton reorganization	Any process that modulates the frequency, rate or extent of actin cytoskeleton reorganization.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0010506	regulation of autophagy	Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:2000145	regulation of cell motility	Any process that modulates the frequency, rate or extent of cell motility.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0051893	regulation of focal adhesion assembly	Any process that modulates the frequency, rate or extent of focal adhesion formation, the establishment and maturation of focal adhesions.
	GO:0007346	regulation of mitotic cell cycle	Any process that modulates the rate or extent of progress through the mitotic cell cycle.
	GO:0007088	regulation of mitotic nuclear division	Any process that modulates the frequency, rate or extent of mitosis.
	GO:0043519	regulation of myosin II filament organization	Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of a bipolar filament composed of myosin II molecules.
	GO:0006940	regulation of smooth muscle contraction	Any process that modulates the frequency, rate or extent of smooth muscle contraction.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006417	regulation of translation	Any process that modulates 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: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:0005884	actin filament	A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0045121	membrane raft	Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
	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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	3bqr
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	DAPK3_HUMAN \| O43293	:	1yrp 2j90 3bhy 5a6n 5a6o

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