1BX6 - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE POTENT NATURAL PRODUCT INHIBITOR BALANOL IN COMPLEX WITH THE CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE

Authors :   N. Narayana, N. -H. Xuong, L. F. Ten Eyck, S. S. Taylor

Date :   13 Oct 98 (Deposition) - 27 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Serine/Threonine-Protein Kinase, Balanol, Conformational Changes, Inhibition, Protein Kinase Pka, Crystal Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Narayana, T. C. Diller, K. Koide, M. E. Bunnage, K. C. Nicolaou, L. L. Brunton, N. H. Xuong, L. F. Ten Eyck, S. S. Taylor
Crystal Structure Of The Potent Natural Product Inhibitor Balanol In Complex With The Catalytic Subunit Of Camp-Dependent Protein Kinase.
Biochemistry V. 38 2367 1999
PubMed-ID: 10029530 | Reference-DOI: 10.1021/BI9820659
(for further references see the PDB file header)

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE
	Chains	:	A
	EC Number	:	2.7.1.37
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CAPK OR PKA

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	BA1	1	Ligand/Ion	BALANOL
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
3	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:50 , THR A:51 , GLY A:52 , SER A:53 , PHE A:54 , GLY A:55 , VAL A:57 , ALA A:70 , LYS A:72 , LEU A:74 , GLU A:91 , GLU A:121 , TYR A:122 , VAL A:123 , GLU A:170 , LEU A:173 , THR A:183 , ASP A:184 , PHE A:187 , HOH A:356	BINDING SITE FOR RESIDUE BA1 A 351

(no "SS Bond" information available for 1BX6)

(no "Cis Peptide Bond" information available for 1BX6)

(no "SAP(SNP)/Variant" information available for 1BX6)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	KAPCA_MOUSE	50-73	1	A:49-72
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	KAPCA_MOUSE	163-175	1	A:162-174
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	KAPCA_MOUSE	299-351	1	A:298-350

(no "Exon" information available for 1BX6)

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
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Chain A from PDB  Type:PROTEIN  Length:339
 aligned with KAPCA_MOUSE | P05132 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:339
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         
          KAPCA_MOUSE    13 QESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF 351
               SCOP domains d1bx6a_ A: cAMP-dependent PK, catalytic subunit                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1bx6A01              1bx6A02 A:33-126,A:318-348 Phosphorylase Kinase; domain 1                                     1bx6A01 A:12-32,A:127-317 Transferase(Phosphotransferase) domain 1                                                                                                                             1bx6A02 A:33-126,A:318-348     -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...........eeeeee.eee..eeeeeeee.....eeeeeeeehhhhhhh..hhhhhhhhhhhhh........eeeeee...eeeeee.......hhhhhhhh....hhhhhhhhhhhhhhhhhhhhh........hhheee.....eee...................hhh..hhhhh.....hhhhhhhhhhhhhhhhh.........hhhhhhhh............hhhhhhhhhh..............hhhhhhh.hhh....hhhhh............................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------AGC_KINASE_CTER  PDB: A:298-350 UniProt: 299-351      PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bx6 A  12 QESVKEFLAKAKEDFLKKWETPSQNTAQLDQFDRIKTLGTGSFGRVMLVKHKESGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVAGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFTEF 350
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191     | 201       211       221       231       241       251       261       271       281       291       301       311       321       331      |341         
                                                                                                                                                                                                                   197-TPO                                                                                                                                      338-SEP

Legend:		→ Mismatch	(orange background)
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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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

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: cAMP-dependent PK, catalytic subunit (75)

Mouse (Mus musculus) [TaxId: 10090] (25)

d1bx6a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

House mouse (Mus musculus) (42)

1bx6A02

A:33-126,A:318-348

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

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

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

House mouse (Mus musculus) (41)

1bx6A01

A:12-32,A:127-317

(no "Pfam Domain" information available for 1BX6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KAPCA_MOUSE | P05132)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004691	cAMP-dependent protein kinase activity	Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of cAMP.
	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:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0034237	protein kinase A regulatory subunit binding	Interacting selectively and non-covalently with one or both of the regulatory subunits of protein kinase A.
	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:0071333	cellular response to glucose 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 glucose stimulus.
	GO:0071374	cellular response to parathyroid hormone 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 parathyroid hormone stimulus.
	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:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0001707	mesoderm formation	The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
	GO:0050804	modulation of chemical synaptic transmission	Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission.
	GO:0051447	negative regulation of meiotic cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle.
	GO:1901621	negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning	Any process that stops, prevents or reduces the frequency, rate or extent of smoothened signaling pathway involved in dorsal/ventral neural tube patterning.
	GO:0001843	neural tube closure	The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	GO:0018107	peptidyl-threonine phosphorylation	The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	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:0071158	positive regulation of cell cycle arrest	Any process that increases 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:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0046827	positive regulation of protein export from nucleus	Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
	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:2000810	regulation of bicellular tight junction assembly	Any process that modulates the frequency, rate or extent of tight junction assembly.
	GO:0043457	regulation of cellular respiration	Any process that modulates the frequency, rate or extent of cellular respiration, the enzymatic release of energy from organic compounds.
	GO:0045667	regulation of osteoblast differentiation	Any process that modulates the frequency, rate or extent of osteoblast differentiation.
	GO:0061136	regulation of proteasomal protein catabolic process	Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds that is mediated by the proteasome.
	GO:0070613	regulation of protein processing	Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein.
	GO:0051966	regulation of synaptic transmission, glutamatergic	Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
	GO:0048240	sperm capacitation	A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium.
	GO:0019433	triglyceride catabolic process	The chemical reactions and pathways resulting in the breakdown of a triglyceride, any triester of glycerol.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0005952	cAMP-dependent protein kinase complex	An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	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:0097546	ciliary base	Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0031514	motile cilium	A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell.
	GO:0031594	neuromuscular junction	The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential.
	GO:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0031588	nucleotide-activated protein kinase complex	A protein complex that possesses nucleotide-dependent protein kinase activity. The nucleotide can be AMP (in S. pombe and human) or ADP (in S. cerevisiae).
	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:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0044853	plasma membrane raft	A membrane raft that is part of the plasma membrane.
	GO:0043234	protein complex	A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
	GO:0097225	sperm midpiece	The highly organized segment of the sperm flagellum which begins at the connecting piece and is characterized by the presence of 9 outer dense fibers (ODFs) that lie outside each of the 9 outer axonemal microtubule doublets and by a sheath of mitochondria that encloses the ODFs and the axoneme; the midpiece terminates about one-fourth of the way down the sperm flagellum at the annulus, which marks the beginning of the principal piece.

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