3DJ6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MOUSE AURORA-A CATALYTIC DOMAIN (ASN186->GLY, LYS240->ARG, MET302->LEU) IN COMPLEX WITH COMPOUND 823.

Authors :   R. A. Elling, D. A. Erlanson, W. Yang, B. T. Tangonan, S. K. Hansen, M. J. Romanowski

Date :   22 Jun 08 (Deposition) - 05 May 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Aurora A, Small-Molecule Inhibitor, Fragment-Based Drug Discovery, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Elling, D. A. Erlanson, W. Yang, B. T. Tangonan, S. K. Hansen, M. J. Romanowski
New Fragment-Based Drug Discovery
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SERINE/THREONINE KINASE 6
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3) STAR CODON+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	AURORA A KINASE DOMAIN, UNP RESIDUES 116-382
	Gene	:	AURKA, STK6
	Mutation	:	YES
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	AURORA-A KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	AK6	1	Ligand/Ion	4-METHOXY-N-PHENYL-3-({3-[(1H-PYRROLO[2,3-B]PYRIDIN-5-YLMETHYL)SULFANYL]PROPANOYL}AMINO)BENZAMIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	AK6	2	Ligand/Ion	4-METHOXY-N-PHENYL-3-({3-[(1H-PYRROLO[2,3-B]PYRIDIN-5-YLMETHYL)SULFANYL]PROPANOYL}AMINO)BENZAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AK6	1	Ligand/Ion	4-METHOXY-N-PHENYL-3-({3-[(1H-PYRROLO[2,3-B]PYRIDIN-5-YLMETHYL)SULFANYL]PROPANOYL}AMINO)BENZAMIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:157 , LYS A:175 , LEU A:191 , GLN A:198 , LEU A:207 , LEU A:221 , LEU A:223 , GLU A:224 , TYR A:225 , ALA A:226 , LEU A:276 , ALA A:286 , PHE A:288 , GLY A:289 , HOH A:472 , HOH A:483	BINDING SITE FOR RESIDUE AK6 A 1

(no "SS Bond" information available for 3DJ6)

(no "Cis Peptide Bond" information available for 3DJ6)

(no "SAP(SNP)/Variant" information available for 3DJ6)

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.	AURKA_MOUSE	130-153	1	A:152-175
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	AURKA_MOUSE	243-255	1	A:265-277

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.	AURKA_MOUSE	130-153	2	A:152-175
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	AURKA_MOUSE	243-255	2	A:265-277

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	AURKA_MOUSE	130-153	1	A:152-175
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	AURKA_MOUSE	243-255	1	A:265-277

(no "Exon" information available for 3DJ6)

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:252
 aligned with AURKA_MOUSE | P97477 from UniProtKB/Swiss-Prot  Length:395

    Alignment length:261
                                   128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 
          AURKA_MOUSE   119 WTLEDFDIGRPLGKGKFGNVYLARERQSKFILALKVLFKTQLEKANVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSNGELKIADFGWSVHAPSSRRTTMCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGMPPFEAHTYQETYRRISRVEFTFPDFVTEGARDLISRLLKHNASQRLTLAEVLEHPWIKANSS 379
               SCOP domains d3dj6a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains 3dj6A01 A:141-229 Phosphorylase Kinase; domain 1                                         3dj6A02 A:230-400 Transferase(Phosphotransferase) domain 1                                                                                                                 - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhh.eeeeee.hhhh..eeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhhhh.........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....---------.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dj6 A 141 WTLEDFDIGRPLGKGKFGNVYLARERQSKFILALKVLFKTQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSRFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSNGELKIADFGW---------TTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGMPPFEAHTYQETYRRISRVEFTFPDFVTEGARDLISRLLKHNASQRLTLAEVLEHPWIKANSS 401
                                   150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 
                                                                                                                                                                               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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

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: automated matches (542)

Mouse (Mus musculus) [TaxId: 10090] (33)

d3dj6a_

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)

Mouse (Mus musculus) (21)

3dj6A01

A:141-229

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

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

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

Mouse (Mus musculus) (21)

3dj6A02

A:230-400

(no "Pfam Domain" information available for 3DJ6)

Asymmetric Unit(hide GO term definitions)

Chain A (AURKA_MOUSE | P97477)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0035174	histone serine kinase activity	Catalysis of the transfer of a phosphate group to a serine residue of a histone. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	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:0004712	protein serine/threonine/tyrosine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine 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.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0009948	anterior/posterior axis specification	The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	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:0030030	cell projection organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0051642	centrosome localization	Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
	GO:0035404	histone-serine phosphorylation	The modification of histones by addition of a phosphate group to a serine residue.
	GO:0051321	meiotic cell cycle	Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
	GO:0000212	meiotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle.
	GO:0000226	microtubule cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
	GO:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	GO:0007100	mitotic centrosome separation	Separation of duplicated centrosome components at the beginning of mitosis. The centriole pair within each centrosome becomes part of a separate microtubule organizing center that nucleates a radial array of microtubules called an aster. The two asters move to opposite sides of the nucleus to form the two poles of the mitotic spindle.
	GO:0007052	mitotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:1990138	neuron projection extension	Long distance growth of a single neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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:1900195	positive regulation of oocyte maturation	Any process that activates or increases the frequency, rate or extent of oocyte maturation.
	GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process	Any process that activates or increases the frequency, rate or extent of the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	GO:0071539	protein localization to centrosome	A process in which a protein is transported to, or maintained at, the centrosome.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	GO:0032465	regulation of cytokinesis	Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
	GO:0031647	regulation of protein stability	Any process that affects the structure and integrity of a protein, altering the likelihood of its degradation or aggregation.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0007057	spindle assembly involved in female meiosis I	The aggregation, arrangement and bonding together of a set of components to form the spindle during meiosis I of a meiotic cell cycle in females. An example of this is found in Drosophila melanogaster.
	GO:0007051	spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
	GO:0043203	axon hillock	Portion of the neuronal cell soma from which the axon originates.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005814	centriole	A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
	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:0032133	chromosome passenger complex	A eukaryotically conserved protein complex that localizes to kinetochores in early mitosis, the spindle mid-zone in anaphase B and to the telophase midbody. It has been proposed that the passenger complex coordinates various events based on its location to different structures during the course of mitosis. Complex members include the BIR-domain-containing protein Survivin, Aurora kinase, INCENP and Borealin.
	GO:0005929	cilium	A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
	GO:0000780	condensed nuclear chromosome, centromeric region	The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	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:0042585	germinal vesicle	The enlarged, fluid filled nucleus of a primary oocyte, the development of which is suspended in prophase I of the first meiotic division between embryohood and sexual maturity.
	GO:0072687	meiotic spindle	A spindle that forms as part of meiosis. Several proteins, such as budding yeast Spo21p, fission yeast Spo2 and Spo13, and C. elegans mei-1, localize specifically to the meiotic spindle and are absent from the mitotic spindle.
	GO:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0015630	microtubule cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
	GO:0005815	microtubule organizing center	An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
	GO:0072686	mitotic spindle	A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
	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:0045120	pronucleus	The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.
	GO:0051233	spindle midzone	The area in the center of the spindle where the spindle microtubules from opposite poles overlap.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
	GO:0031616	spindle pole centrosome	A centrosome from which one pole of a mitotic or meiotic spindle is organized.

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	3dj6
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	AURKA_MOUSE \| P97477
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	2.7.11.1
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	AURKA_MOUSE \| P97477
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UniProtKB/Swiss-Prot
	AURKA_MOUSE \| P97477	:	3d14 3d15 3d2i 3d2k 3daj 3dj5 3dj7

2c6d	AURORA A KINASE ACTIVATED MUTANT (T287D) IN COMPLEX WITH ADPNP
3d14	SAME PROTEIN COMPLEXED WITH INHIBITOR AK1
3d15	SAME PROTEIN COMPLEXED WITH INHIBITOR AK2
3d2i	SAME PROTEIN COMPLEXED WITH INHIBITOR AK3
3d2k	SAME PROTEIN COMPLEXED WITH INHIBITOR AK4
3dj5	SAME PROTEIN COMPLEXED WITH INHIBITOR AK5
3dj7	SAME PROTEIN COMPLEXED WITH INHIBITOR AK7

Description

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Ligands, Modified Residues, Ions (1, 1)

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SCOP Domains (1, 1)

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