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(-) Description

Title :  STRUCTURE OF THE REGULATORY FRAGMENT OF SACCHAROMYCES CEREVISIAE AMPK IN COMPLEX WITH ADP
 
Authors :  F. V. Mayer, R. Heath, E. Underwood, M. J. Sanders, D. Carmena, R. Mccart F. C. Leiper, B. Xiao, C. Jing, P. A. Walker, L. F. Haire, R. Ogrodowicz, S. R. Martin, M. C. Schmdit, S. J. Gamblin, D. Carling
Date :  26 Jul 11  (Deposition) - 09 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cbs Domain, Nucleotide Binding, Cytosol, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. V. Mayer, R. Heath, E. Underwood, M. J. Sanders, D. Carmena, R. R. Mccartney, F. C. Leiper, B. Xiao, C. Jing, P. A. Walker, L. F. Haire R. Ogrodowicz, S. R. Martin, M. C. Schmidt, S. J. Gamblin, D. Carling
Adp Regulates Snf1, The Saccharomyces Cerevisiae Homolog Of Amp-Activated Protein Kinase.
Cell Metab V. 14 707 2011
PubMed-ID: 22019086  |  Reference-DOI: 10.1016/J.CMET.2011.09.009

(-) Compounds

Molecule 1 - CARBON CATABOLITE-DEREPRESSING PROTEIN KINASE
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSNF1, CAT1, CCR1, GLC2, PAS14, YDR477W, D8035.20
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
 
Molecule 2 - SNF1 PROTEIN KINASE SUBUNIT BETA-2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSIP2, SPM2, YGL208W, G1155
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymPROTEIN SPM2, SNF1-INTERACTING PROTEIN 2
 
Molecule 3 - NUCLEAR PROTEIN SNF4
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneSNF4, CAT3, YGL115W
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymREGULATORY PROTEIN CAT3

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN C:168 , THR C:196 , ASN C:199 , MET C:200 , LYS C:201 , VAL C:221 , SER C:222 , SER C:223 , PRO C:225 , THR C:310 , SER C:312 , ASP C:313 , HOH C:394 , HOH C:397 , HOH C:406 , HOH C:417BINDING SITE FOR RESIDUE ADP C 324

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T4N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T4N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T4N)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.AAKG_YEAST37-97
118-181
194-253
262-322
  4C:38-98
C:119-182
C:195-254
C:263-322

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR477W1YDR477W.1IV:1412366-14142671902SNF1_YEAST1-6336331A:465-630 (gaps)166

2.1YGL115W1YGL115W.1VII:292036-293004969AAKG_YEAST1-3223221C:8-322 (gaps)315

3.1YGL208W1YGL208W.1VII:97342-985891248SIP2_YEAST1-4154151B:303-413 (gaps)111

(-) 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:139
 aligned with SNF1_YEAST | P06782 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:166
                                   474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624      
           SNF1_YEAST   465 STVSILPTSLPQIHRANMLAQGSPAASKISPLVTKKSKTRWHFGIRSRSYPLDVMGEIYIALKNLGAEWAKPSEEDLWTIKLRWKYDIGNKTNTNEKIPDLMKMVIQLFQIETNNYLVDFKFDGWESSYGDDTTVSNISEDEMSTFSAYPFLHLTTKLIMELAVNS 630
               SCOP domains d3t4na_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.hhhhhhhhhhhhhhhh.hhhhhh............ee.eee..hhhhhhhhhhhhhhhhh.eee..hhhhh.eeeeee..-----------...eeeeeeeeeeee..eeeeeeeeeeee.----------------....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:465-630 (gaps) UniProt: 1-633 [INCOMPLETE]                                                                                                            Transcript 1
                 3t4n A 465 STVSILPTSLPQIHRANMLAQGSPAASKISPLVTKKSKTRWHFGIRSRSYPLDVMGEIYIALKNLGAEWAKPSEEDLWTIKLRWKY-----------IPDLMKMVIQLFQIETNNYLVDFKFDGWES----------------STFSAYPFLHLTTKLIMELAVNS 630
                                   474       484       494       504       514       524       534       544     |   -       564       574       584      |  -         -   |   614       624      
                                                                                                               550         562                          591              608                      

Chain B from PDB  Type:PROTEIN  Length:104
 aligned with SIP2_YEAST | P34164 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:111
                                   312       322       332       342       352       362       372       382       392       402       412 
           SIP2_YEAST   303 LEYTTDIPAVFTDPSVMERYYYTLDRQQSNTDTSWLTPPQLPPQLENVILNKYYATQDQFNENNSGALPIPNHVVLNHLVTSSIKHNTLCVASIVRYKQKYVTQILYTPIE 413
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...hhhhhhhhhhhhhhhh..-------hhhhh....hhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...ee......eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 3 Exon 3.1  PDB: B:303-413 (gaps) UniProt: 1-415 [INCOMPLETE]                                                     Transcript 3
                 3t4n B 303 MEYTTDIPAVFTDPSVMERYYYTLD-------TSWLTPPQLPPQLENVILNKYYATQDQFNENNSGALPIPNHVVLNHLVTSSIKHNTLCVASIVRYKQKYVTQILYTPIE 413
                                   312       322    |    -  |    342       352       362       372       382       392       402       412 
                                                  327     335                                                                              

Chain C from PDB  Type:PROTEIN  Length:311
 aligned with AAKG_YEAST | P12904 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:315
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316     
           AAKG_YEAST     7 SQEKVSIEQQLAVESIRKFLNSKTSYDVLPVSYRLIVLDTSLLVKKSLNVLLQNSIVSAPLWDSKTSRFAGLLTTTDFINVIQYYFSNPDKFELVDKLQLDGLKDIERALGVDQLDTASIHPSRPLFEACLKMLESRSGRIPLIDQDEETHREIVVSVLTQYRILKFVALNCRETHFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGS 321
               SCOP domains d3t4nc1 C:8-186 automated matches                                                                                                                                                  d3t4nc2 C:187-322 automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh....eeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----........hhhhhhhhhhhhh..eeeeeee......eeeeeeeehhhhhhhhhhhhhhhhhh..hhhhh...............hhhhhhhhhhhhh..eeeee.....eeeeee.hhhhhhhhhhhhhhh..hhhhhhhhh.......eee....hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------CBS  PDB: C:38-98 UniProt: 37-97                             --------------------CBS  PDB: C:119-182 UniProt: 118-181                            ------------CBS  PDB: C:195-254 UniProt: 194-253                        --------CBS  PDB: C:263-322 UniProt: 262-322                         PROSITE
               Transcript 2 Exon 2.1  PDB: C:8-322 (gaps) UniProt: 1-322 [INCOMPLETE]                                                                                                                                                                                                                                                                   Transcript 2
                 3t4n C   8 SQEKVSIEQQLAVESIRKFLNSKTSYDVLPVSYRLIVLDTSLLVKKSLNVLLQNSIVSAPLWDSKTSRFAGLLTTTDFINVIQYYFSNPDKFELVDKLQLDGLKDIERALGV----TASIHPSRPLFEACLKMLESRSGRIPLIDQDEETHREIVVSVLTQYRILKFVALNCRETHFLKIPIGDLNIITQDNMKSCQMTTPVIDVIQMLTQGRVSSVPIIDENGYLINVYEAYDVLGLIKGGIYNDLSLSVGEALMRRSDDFEGVYTCTKNDKLSTIMDNIRKARVHRFFVVDDVGRLVGVLTLSDILKYILLGS 322
                                    17        27        37        47        57        67        77        87        97       107       117 |    |127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317     
                                                                                                                                         119  124                                                                                                                                                                                                      

   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  (2, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T4N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T4N)

(-) Gene Ontology  (44, 65)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SNF1_YEAST | P06782)
molecular function
    GO:0004679    AMP-activated protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP.
    GO:0005086    ARF guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with the GTPase ARF. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0006995    cellular response to nitrogen starvation    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 deprivation of nitrogen.
    GO:0071940    fungal-type cell wall assembly    The aggregation, arrangement and bonding together of a set of components to form a fungal-type cell wall.
    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:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:1900436    positive regulation of filamentous growth of a population of unicellular organisms in response to starvation    Any process that activates or increases the frequency, rate or extent of filamentous growth of a population of unicellular organisms in response to starvation.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0016239    positive regulation of macroautophagy    Any process, such as recognition of nutrient depletion, that activates or increases the rate of macroautophagy to bring cytosolic macromolecules to the vacuole/lysosome for degradation.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007124    pseudohyphal growth    A pattern of cell growth that occurs in conditions of nitrogen limitation and abundant fermentable carbon source. Cells become elongated, switch to a unipolar budding pattern, remain physically attached to each other, and invade the growth substrate.
    GO:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    GO:0006986    response to unfolded protein    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 an unfolded protein stimulus.
    GO:0090606    single-species surface biofilm formation    A process in which planktonically growing microorganisms of the same species grow at the surface of a liquid-air interface and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000324    fungal-type vacuole    A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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.

Chain B   (SIP2_YEAST | P34164)
molecular function
    GO:0004679    AMP-activated protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP.
    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).
biological process
    GO:0042149    cellular response to glucose starvation    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 deprivation of glucose.
    GO:0001403    invasive growth in response to glucose limitation    A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0043254    regulation of protein complex assembly    Any process that modulates the frequency, rate or extent of protein complex assembly.
    GO:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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: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.

Chain C   (AAKG_YEAST | P12904)
molecular function
    GO:0004679    AMP-activated protein kinase activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires the presence of AMP.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0007031    peroxisome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a peroxisome. A peroxisome is a small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules.
    GO:0045722    positive regulation of gluconeogenesis    Any process that activates or increases the frequency, rate or extent of gluconeogenesis.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0001302    replicative cell aging    The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005641    nuclear envelope lumen    The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
    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.

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 Related Entries

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

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        AAKG_YEAST | P129042nyc 2nye 2qlv 3tdh 3te5
        SIP2_YEAST | P341642qlv 3tdh 3te5
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(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3T4N)