1NY3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ADP BOUND TO MAP KAP KINASE 2

Authors :   K. W. Underwood, K. D. Parris, E. Federico, L. Mosyak, T. Shane, M. Taylo K. Svenson, Y. Liu, C. L. Hsiao, S. Wolfrom, M. Maguire, K. Malakian, J. B. Telliez, L. L. Lin, R. W. Kriz, J. Seehra, W. S. Somers, M. L. Stahl

Date :   11 Feb 03 (Deposition) - 14 Oct 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (12x)

Keywords :   Map Kap Kinase 2, Mk2, Adp, Kinase, Ser/Thr Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. W. Underwood, K. D. Parris, E. Federico, L. Mosyak, R. M. Czerwinski T. Shane, M. Taylor, K. Svenson, Y. Liu, C. L. Hsiao, S. Wolfrom, M. Maguire, K. Malakian, J. B. Telliez, L. L. Lin, R. W. Kriz, J. Seehra, W. S. Somers, M. L. Stahl
Catalytically Active Map Kap Kinase 2 Structures In Complex With Staurosporine And Adp Reveal Differences With The Autoinhibited Enzyme
Structure V. 11 627 2003
PubMed-ID: 12791252 | Reference-DOI: 10.1016/S0969-2126(03)00092-3

Molecule 1 - MAP KINASE-ACTIVATED PROTEIN KINASE 2
	Chains	:	A
	EC Number	:	2.7.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MAPKAPK2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MAPK-ACTIVATED PROTEIN KINASE 2, MAPKAP KINASE 2, MAPKAPK-2

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (12x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 12)

No.	Name	Count	Type	Full Name
1	ADP	12	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:70 , GLY A:71 , LEU A:72 , GLY A:73 , ILE A:74 , ALA A:91 , LYS A:93 , GLU A:139 , LEU A:141 , ASN A:191 , ASP A:207	BINDING SITE FOR RESIDUE ADP A 401

(no "SS Bond" information available for 1NY3)

Asymmetric Unit

No.	Residues
1	Ser A:216	-	His A:217
2	Asn A:288	-	Pro A:289

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040753	A	173	G	MAPK2_HUMAN	Polymorphism	35671930	A	A	173	G

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040753	A	173	G	MAPK2_HUMAN	Polymorphism	35671930	A	A	173	G

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

Biological Unit 2 (1, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040753	A	173	G	MAPK2_HUMAN	Polymorphism	35671930	A	A	173	G

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.	MAPK2_HUMAN	70-93	1	A:70-93
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MAPK2_HUMAN	182-194	1	A:182-194

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MAPK2_HUMAN	70-93	1	A:70-93
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MAPK2_HUMAN	182-194	1	A:182-194

Biological Unit 2 (2, 24)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	MAPK2_HUMAN	70-93	12	A:70-93
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MAPK2_HUMAN	182-194	12	A:182-194

Asymmetric Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000367103	1b	ENSE00001825387	chr1:206858382-206858853	472	MAPK2_HUMAN	1-93	93	1	A:46-93	48
1.2	ENST00000367103	2	ENSE00001069545	chr1:206902055-206902194	140	MAPK2_HUMAN	94-140	47	1	A:94-140	47
1.3b	ENST00000367103	3b	ENSE00001069547	chr1:206902380-206902444	65	MAPK2_HUMAN	140-162	23	1	A:140-162 (gaps)	23
1.4b	ENST00000367103	4b	ENSE00001069548	chr1:206902741-206902820	80	MAPK2_HUMAN	162-188	27	1	A:162-188	27
1.5	ENST00000367103	5	ENSE00001069551	chr1:206903317-206903443	127	MAPK2_HUMAN	189-231	43	1	A:189-231 (gaps)	43
1.6	ENST00000367103	6	ENSE00001648220	chr1:206904033-206904108	76	MAPK2_HUMAN	231-256	26	1	A:231-256	26
1.7	ENST00000367103	7	ENSE00001069544	chr1:206904483-206904607	125	MAPK2_HUMAN	256-298	43	1	A:256-298 (gaps)	43
1.8b	ENST00000367103	8b	ENSE00001069550	chr1:206904985-206905070	86	MAPK2_HUMAN	298-326	29	1	A:298-326	29
1.9b	ENST00000367103	9b	ENSE00001069552	chr1:206905184-206905264	81	MAPK2_HUMAN	327-353	27	1	A:327-345	19
1.9d	ENST00000367103	9d	ENSE00001443498	chr1:206905920-206907628	1709	MAPK2_HUMAN	354-400	47	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:277
 aligned with MAPK2_HUMAN | P49137 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:300
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345
          MAPK2_HUMAN    46 FHVKSGLQIKKNAIIDDYKVTSQVLGLGINGKVLQIFNKRTQEKFALKMLQDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECLDGGELFSRIQDRGDQAFTEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRPNAILKLTDFGFAKETTSHNSLTTPCYTPYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYSNHGLAISPGMKTRIRMGQYEFPNPEWSEVSEEVKMLIRNLLKTEPTQRMTITEFMNHPWIMQSTKVPQTPLHTSRVLKED 345
               SCOP domains d1ny3a_ A: MAP kinase activated protein kinase 2, mapkap2                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -------------1ny3A01 A:59-140 Phosphorylase Kinase; domain 1                                   1ny3A02 A:14      1-342 Transferase(Phosphotransferase) domain 1                                                                                                                                          --- CATH domains
               Pfam domains ------------------Pkinase-1ny3A01 A:64-325                                                                                                                                                                                                                                              -------------------- Pfam domains
         Sec.struct. author ........ee..hhhhheeeeeeeeeee..eeeeeeee.....eeeeeeee.hhhhhhhhhhhhh.........eeeeeeeee..eeeeeeeee....eehhhhhhh------hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee........eee......ee....---------...............hhhhhhhhhhhhhhhhhh......--------hhhhhhhh.............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------PROTEIN_KINASE_ATP      ----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:46-93 UniProt: 1-93           Exon 1.2  PDB: A:94-140 UniProt: 94-140        ---------------------Exon 1.4b  PDB: A:162-188  Exon 1.5  PDB: A:189-231 (gaps)            ------------------------Exon 1.7  PDB: A:256-298 (gaps)            ----------------------------Exon 1.9b           Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.3b              --------------------------------------------------------------------Exon 1.6  PDB: A:231-256  -----------------------------------------Exon 1.8b  PDB: A:298-326    ------------------- Transcript 1 (2)
                 1ny3 A  46 FHVKSGLQIKKNAIIDDYKVTSQVLGLGINGKVLQIFNKRTQEKFALKMLQDCPKARREVELHWRASQCPHIVRIVDVYENLYAGRKCLLIVMECLDGGELFSRIQD------TEREASEIMKSIGEAIQYLHSINIAHRDVKPENLLYTSKRPNAILKLTDFGFAKETTSH---------PYYVAPEVLGPEKYDKSCDMWSLGVIMYILLCGYPPFYS--------GMKTRIRMGQYEFPNPEWSEVSEEVKMLIRNLLKTEPTQRMTITEFMNHPWIMQSTKVPQTPLHTSRVLKED 345
                                    55        65        75        85        95       105       115       125       135       145      |  -   |   165       175       185       195       205       215 |       - |     235       245       255       265       275       285       295       305       315       325       335       345
                                                                                                                                    152    159                                                       217       227                                   265      274

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

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: Protein kinases, catalytic subunit (1977)

Protein domain: MAP kinase activated protein kinase 2, mapkap2 (14)

Human (Homo sapiens) [TaxId: 9606] (14)

d1ny3a_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

1ny3A01

A:59-140

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)

1ny3A02

A:141-342

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Homo sapiens (Human) (521)

Pkinase-1ny3A01

A:64-325

Asymmetric Unit(hide GO term definitions)

Chain A (MAPK2_HUMAN | P49137)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0009931	calcium-dependent protein serine/threonine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions are dependent on the presence of calcium ions.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0004683	calmodulin-dependent protein kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
	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:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	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:0070935	3'-UTR-mediated mRNA stabilization	An mRNA stabilization process in which one or more RNA-binding proteins associate with the 3'-untranslated region (UTR) of an mRNA.
	GO:0031572	G2 DNA damage checkpoint	A cell cycle checkpoint that detects and negatively regulates progression from G2 to M phase in the cell cycle in response to DNA damage.
	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:0007265	Ras protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Ras superfamily of proteins switching to a GTP-bound active state.
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	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:0035924	cellular response to vascular endothelial growth factor 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 vascular endothelial growth factor stimulus.
	GO:0006954	inflammatory response	The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
	GO:0048839	inner ear development	The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
	GO:0006691	leukotriene metabolic process	The chemical reactions and pathways involving leukotriene, a pharmacologically active substance derived from a polyunsaturated fatty acid, such as arachidonic acid.
	GO:0048255	mRNA stabilization	Prevention of degradation of mRNA molecules. In the absence of compensating changes in other processes, the slowing of mRNA degradation can result in an overall increase in the population of active mRNA molecules.
	GO:0044351	macropinocytosis	An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
	GO:0038066	p38MAPK cascade	An intracellular protein kinase cascade containing at least a p38 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:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	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:0042535	positive regulation of tumor necrosis factor biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
	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:1900034	regulation of cellular response to heat	Any process that modulates the frequency, rate or extent of cellular response to heat.
	GO:0032675	regulation of interleukin-6 production	Any process that modulates the frequency, rate, or extent of interleukin-6 production.
	GO:0043488	regulation of mRNA stability	Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
	GO:0032680	regulation of tumor necrosis factor production	Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
	GO:0034097	response to cytokine	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 cytokine stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0006950	response to stress	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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0002224	toll-like receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a toll-like receptor. Toll-like receptors directly bind pattern motifs from a variety of microbial sources to initiate innate immune response.
	GO:0048010	vascular endothelial growth factor receptor signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005813	centrosome	A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
	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:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

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	1ny3
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	MAPK2_HUMAN \| P49137
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	2.7.1.-
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1nxk	CRYSTAL STRUCTURE OF STAUROSPORINE BOUND TO MAP KAP KINASE 2

Description

Compounds

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

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Exons (9, 9)

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