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(-) Description

Authors :  D. Lavogina, N. Koenig, A. Uri, D. Bossemeyer
Date :  09 Jan 08  (Deposition) - 03 Feb 09  (Release) - 13 Jul 11  (Revision)
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Bisubstrate Inhibitor, Protein Kinase, Serine/Threonine-Protein Kinase, Atp-Binding, Camp, Phosphoprotein, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  D. Lavogina, M. Lust, I. Viil, N. Konig, G. Raidaru, J. Rogozina, E. Enkvist, A. Uri, D. Bossemeyer
Structural Analysis Of Arc-Type Inhibitor (Arc-1034) Bindin To Protein Kinase A Catalytic Subunit And Rational Design O Bisubstrate Analogue Inhibitors Of Basophilic Protein Kinases.
J. Med. Chem. V. 52 308 2009
PubMed-ID: 19143565  |  Reference-DOI: 10.1021/JM800797N
(for further references see the PDB file header)

(-) Compounds

    EC Number2.7.11.11
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System StrainBL21DE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymPKA C-ALPHA

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWARELEU A:49 , THR A:51 , GLY A:52 , SER A:53 , PHE A:54 , GLY A:55 , ALA A:70 , LYS A:72 , MET A:120 , GLU A:121 , TYR A:122 , GLU A:127 , ASP A:166 , LYS A:168 , GLU A:170 , LEU A:173 , THR A:183 , ASP A:184 , PHE A:187 , THR A:201 , PHE A:327 , HOH A:404 , HOH A:457 , HOH A:503BINDING SITE FOR RESIDUE ARX A 351
2AC2SOFTWARELYS A:83 , GLN A:84 , ILE A:85 , GLU A:86 , ASN A:90 , ARG A:133 , ILE A:135 , GLY A:136 , ARG A:137 , LYS A:189 , ALA A:233 , GLY A:234 , TYR A:235 , HOH A:402 , HOH A:417 , HOH A:428 , HOH A:446 , HOH A:454 , HOH A:516 , HOH A:550 , HOH A:582BINDING SITE FOR RESIDUE ARX A 352

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.KAPCA_BOVIN50-73  1A:49-72
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.KAPCA_BOVIN163-175  1A:162-174
3AGC_KINASE_CTERPS51285 AGC-kinase C-terminal domain profile.KAPCA_BOVIN299-351  1A:298-350

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

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:341
 aligned with KAPCA_BOVIN | P00517 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:341
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
               SCOP domains d3bwja_ A: cAMP-dependent PK, catalytic subunit                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -----3bwjA01           3bwjA02 A:33-126,A:318-348 Phosphorylase Kinase; domain 1                                     3bwjA01 A:15-32,A:127-317 Transferase(Phosphotransferase) domain 1                                                                                                                             3bwjA02 A:33-126,A:318-348     -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author 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)
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349 
                                                                                                                                                           139-SEP                                                   197-TPO                                                                                                                                      338-SEP        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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.


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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        KAPCA_BOVIN | P005171cdk 1cmk 1kmu 1kmw 1q24 1q61 1q62 1q8t 1q8u 1q8w 1smh 1stc 1sve 1svg 1svh 1szm 1veb 1xh4 1xh5 1xh6 1xh7 1xh8 1xh9 1xha 1ydr 1yds 1ydt 2c1a 2c1b 2f7e 2f7x 2f7z 2gfc 2gnf 2gng 2gnh 2gni 2gnj 2gnl 2jds 2jdt 2jdv 2oh0 2ojf 2uvx 2uvy 2uvz 2uw0 2uw3 2uw4 2uw5 2uw6 2uw7 2uw8 2uzt 2uzu 2uzv 2uzw 2vnw 2vny 2vo0 2vo3 2vo6 2vo7 3ag9 3dnd 3dne 3e8c 3e8e 3kkv 3zo1 3zo2 3zo3 3zo4 4axa 4c33 4c34 4c35 4c36 4c37 4c38 4ie9 4ij9 4yxr 4yxs 4z83 4z84

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BWJ)