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Asym./Biol. Unit (Jmol Viewer)

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Title :   CAMP-DEPENDENT PROTEIN KINASE PKA CATALYTIC SUBUNIT WITH PKI-5-24

Authors :   A. Schiffer, K. U. Wendt

Date :   02 Jul 08 (Deposition) - 23 Jun 09 (Release) - 09 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,I

Keywords :   Atp-Binding, Kinase, Lipoprotein, Myristate, Nucleotide-Binding, Nucleus, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Camp, Protein Kinase Inhibitor, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Orts, J. Tuma, M. Reese, S. K. Grimm, P. Monecke, S. Bartoschek, A. Schiffer, K. U. Wendt, C. Griesinger, T. Carlomagno
Crystallography-Independent Determination Of Ligand Binding Modes
Angew. Chem. Int. Ed. Engl. V. 47 7736 2008
PubMed-ID: 18767090 | Reference-DOI: 10.1002/ANIE.200801792

Molecule 1 - CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
	Chains	:	A
	EC Number	:	2.7.11.11
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	PKA C-ALPHA

Molecule 2 - CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
	Chains	:	I
	Engineered	:	YES
	Fragment	:	INHIBITORY FRAGMENT, UNP RESIDUES 6-25
	Other Details	:	SYNTHETIC CONSTRUCT
	Synonym	:	CAMP-DEPENDENT PROTEIN KINASE INHIBITOR, MUSCLE/BRAIN ISOFORM, PKI-ALPHA
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	I

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	LL1	1	Ligand/Ion	3-PYRIDIN-4-YL-1H-INDAZOLE
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
3	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:49 , ALA A:70 , GLU A:121 , TYR A:122 , VAL A:123 , LEU A:173 , THR A:183 , ASP A:184 , PHE A:327	BINDING SITE FOR RESIDUE LL1 A 351
2	AC2	SOFTWARE	LYS A:83 , GLN A:84 , GLU A:86 , LEU A:89 , ARG A:93 , GLU A:127 , PHE A:129 , SER A:130 , ARG A:133 , LYS A:168 , PRO A:169 , GLU A:170 , PHE A:187 , LYS A:189 , ARG A:190 , VAL A:191 , LYS A:192 , LEU A:198 , CYS A:199 , GLY A:200 , THR A:201 , PRO A:202 , GLU A:203 , GLU A:230 , GLY A:234 , TYR A:235 , PRO A:236 , PHE A:239 , ALA A:240 , ASP A:241 , ILE A:246 , ASP A:328 , GLU A:349 , HOH A:355 , HOH A:370 , HOH A:478 , HOH I:25 , HOH I:26 , HOH I:27 , HOH I:28 , HOH I:29 , HOH I:30 , HOH I:31 , HOH I:32 , HOH I:33 , HOH I:34 , HOH I:35 , HOH I:36 , HOH I:37 , HOH I:38 , HOH I:39 , HOH I:41 , HOH I:42 , HOH I:44 , HOH I:45 , HOH I:47 , HOH I:48 , HOH I:52 , HOH I:54	BINDING SITE FOR CHAIN I OF CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA

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

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

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

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_BOVIN	50-73	1	A:49-72
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	KAPCA_BOVIN	163-175	1	A:162-174
3	AGC_KINASE_CTER	PS51285	AGC-kinase C-terminal domain profile.	KAPCA_BOVIN	299-351	1	A:298-350

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000008727	1	ENSBTAE00000070584	chr7:9765104-9765150	47	KAPCA_BOVIN	1-16	16	1	A:13-15	3
1.2	ENSBTAT00000008727	2	ENSBTAE00000389552	chr7:9773081-9773142	62	KAPCA_BOVIN	16-36	21	1	A:15-35	21
1.3	ENSBTAT00000008727	3	ENSBTAE00000070589	chr7:9773591-9773719	129	KAPCA_BOVIN	37-79	43	1	A:36-78	43
1.4	ENSBTAT00000008727	4	ENSBTAE00000070592	chr7:9775980-9776078	99	KAPCA_BOVIN	80-112	33	1	A:79-111	33
1.5	ENSBTAT00000008727	5	ENSBTAE00000425416	chr7:9777080-9777162	83	KAPCA_BOVIN	113-140	28	1	A:112-139	28
1.6	ENSBTAT00000008727	6	ENSBTAE00000070601	chr7:9778181-9778307	127	KAPCA_BOVIN	140-182	43	1	A:139-181	43
1.7	ENSBTAT00000008727	7	ENSBTAE00000070605	chr7:9778400-9778495	96	KAPCA_BOVIN	183-214	32	1	A:182-213	32
1.8	ENSBTAT00000008727	8	ENSBTAE00000070609	chr7:9778596-9778718	123	KAPCA_BOVIN	215-255	41	1	A:214-254	41
1.9	ENSBTAT00000008727	9	ENSBTAE00000427228	chr7:9780756-9780920	165	KAPCA_BOVIN	256-310	55	1	A:255-309	55
1.10	ENSBTAT00000008727	10	ENSBTAE00000383679	chr7:9781489-9781832	344	KAPCA_BOVIN	311-351	41	1	A:310-350	41

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:338
 aligned with KAPCA_BOVIN | P00517 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:338
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343        
          KAPCA_BOVIN    14 ESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF 351
               SCOP domains d3dnea_ A: cAMP-dependent PK, catalytic subunit                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3dneA01             3dneA02 A:33-126,A:318-348 Phosphorylase Kinase; domain 1                                     3dneA01 A:13-32,A:127-317 Transferase(Phosphotransferase) domain 1                                                                                                                             3dneA02 A:33-126,A:318-348     -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh......hhh.eeeeeeeee...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........eehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh........................................... 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 1 (1) 1.1--------------------Exon 1.3  PDB: A:36-78 UniProt: 37-79      Exon 1.4  PDB: A:79-111          Exon 1.5  PDB: A:112-139    ------------------------------------------Exon 1.7  PDB: A:182-213        Exon 1.8  PDB: A:214-254 UniProt: 215-255Exon 1.9  PDB: A:255-309 UniProt: 256-310              Exon 1.10  PDB: A:310-350                 Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: A:15-3-------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:139-181 UniProt: 140-182  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3dne A  13 ESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHMETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWtLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVsINEKCGKEFSEF 350
                                    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        
                                                                                                                                                                                                                  197-TPO                                                                                                                                      338-SEP

Chain I from PDB  Type:PROTEIN  Length:20
 aligned with IPKA_RABIT | P61926 from UniProtKB/Swiss-Prot  Length:76

    Alignment length:20
                                    15        25
           IPKA_RABIT     6 TTYADFIASGRTGRRNAIHD  25
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author hhhhhhhh.........ee. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 3dne I   5 TTYADFIASGRTGRRNAIHD  24
                                    14        24

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

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

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

Family: Protein kinases, catalytic subunit (1977)

Protein domain: cAMP-dependent PK, catalytic subunit (75)

Cow (Bos taurus) [TaxId: 9913] (39)

d3dnea_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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)

Bovine,cow,domestic cattle,domestic cow (Bos taurus) (2)

3dneA02

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)

Bovine,cow,domestic cattle,domestic cow (Bos taurus) (2)

3dneA01

A:13-32,A:127-317

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KAPCA_BOVIN | P00517)

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: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: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: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: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: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: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.
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: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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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: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: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: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.

Chain I (IPKA_RABIT | P61926)

molecular function
	GO:0004862	cAMP-dependent protein kinase inhibitor activity	Stops, prevents or reduces the activity of a cAMP-dependent protein kinase.
	GO:0004860	protein kinase inhibitor activity	Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0071901	negative regulation of protein serine/threonine kinase activity	Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.

Asymmetric/Biological Unit
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	2.7.11.11
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (10, 10)

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