Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Theor.Model - manually
(-)Theoretical Model
collapse expand < >
Image Theor.Model - manually
Theor.Model - manually  (Jmol Viewer)
Image Theoretical Model
Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MOLECULAR MODELED STRUCTURE OF GLYCOGEN SYNTHASE KINASE 3 ALPHA [HOMO SAPIENS]
 
Authors :  Anooprajk, N. Pradhan
Date :  03 Mar 06  (Deposition) - 21 Mar 06  (Release) - 21 Mar 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Serine/Threonine Protein Kinases, Catalytic Domain" (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Anooprajk, N. Pradhan
Molecular Modeled Structure Of Glycogen Synthase Kinase 3 Alpha [Homo Sapiens]
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOGEN SYNTHASE KINASE-3 ALPHA
    ChainsA
    EC Number2.7.1.37
    FragmentATP BINDING, PROTEIN KINASE, RESIDUES 1-352
    GenusGSK3A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Other DetailsBRAIN
    SynonymGSK-3 ALPHA

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2DFM)

(-) Sites  (0, 0)

(no "Site" information available for 2DFM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DFM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DFM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Theoretical Model (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051625Q109EGSK3A_HUMANPolymorphism35978177AQ12E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.GSK3A_HUMAN125-149  1A:28-52
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.GSK3A_HUMAN240-252  1A:143-155

(-) Exons   (9, 9)

Theoretical Model (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002223301bENSE00001053028chr19:42746745-42746335411GSK3A_HUMAN1-95950--
1.2bENST000002223302bENSE00000847272chr19:42744294-42744107188GSK3A_HUMAN95-157631A:1-6060
1.3ENST000002223303ENSE00000709432chr19:42741093-4274101084GSK3A_HUMAN158-185281A:61-8828
1.4ENST000002223304ENSE00000709433chr19:42740868-42740758111GSK3A_HUMAN186-222371A:89-12537
1.5ENST000002223305ENSE00000709434chr19:42738830-42738700131GSK3A_HUMAN223-266441A:126-16944
1.6ENST000002223306ENSE00000709435chr19:42738611-42738505107GSK3A_HUMAN266-302371A:169-20537
1.7ENST000002223307ENSE00000709436chr19:42737535-4273743898GSK3A_HUMAN302-334331A:205-23733
1.8ENST000002223308ENSE00000709437chr19:42737357-4273726296GSK3A_HUMAN335-366321A:238-26932
1.9bENST000002223309bENSE00000709438chr19:42736834-42736648187GSK3A_HUMAN367-429631A:270-33263
1.10ENST0000022233010ENSE00000709439chr19:42736301-4273620993GSK3A_HUMAN429-460321A:332-35221
1.11dENST0000022233011dENSE00001910351chr19:42735019-42734338682GSK3A_HUMAN460-483240--

(-) Sequences/Alignments

Theoretical Model
   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:352
 aligned with GSK3A_HUMAN | P49840 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:352
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447  
          GSK3A_HUMAN    98 GKVTTVVATLGQGPERSQEVAYTDIKVIGNGSFGVVYQARLAETRELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDELYLNLVLEYVPETVYRVARHFTKAKLTIPILYVKVYMYQLFRSLAYIHSQGVCHRDIKPQNLLVDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFKSRTPPEAIALCSSLLEYTPSSRLSPLEACAHSFFDELRCLGTQLPNNRPLPPLFNFSAGELSIQPSLNAILIPPHLRSPA 449
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......eeeeeeeeeeeeee....eeeeeee.....eeeeeeeee.....hhhhhhhhhh.......eeeeeeee......eeeeeeee...eehhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eee......eee.hhhhhee............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh...............hhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.................hhhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------E---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PROTEIN_KINASE_ATP       ------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:1-60 UniProt: 95-157 [INCOMPLETE]         Exon 1.3  PDB: A:61-88      Exon 1.4  PDB: A:89-125              Exon 1.5  PDB: A:126-169 UniProt: 223-266   -----------------------------------Exon 1.7  PDB: A:205-237         Exon 1.8  PDB: A:238-269        --------------------------------------------------------------Exon 1.10             Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:169-205             ----------------------------------------------------------------Exon 1.9b  PDB: A:270-332 UniProt: 367-429                     -------------------- Transcript 1 (2)
                 2dfm A   1 GKVTTVVATLGQGPERSQEVAYTDIKVIGNGSFGVVYQARLAETRELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDELYLNLVLEYVPETVYRVARHFTKAKLTIPILYVKVYMYQLFRSLAYIHSQGVCHRDIKPQNLLVDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFKSRTPPEAIALCSSLLEYTPSSRLSPLEACAHSFFDELRCLGTQLPNNRPLPPLFNFSAGELSIQPSLNAILIPPHLRSPA 352
                                    10        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  

   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  (0, 0)

(no "SCOP Domain" information available for 2DFM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DFM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DFM)

(-) Gene Ontology  (48, 48)

Theoretical Model(hide GO term definitions)
Chain A   (GSK3A_HUMAN | P49840)
molecular function
    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:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic 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: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:0050321    tau-protein kinase activity    Catalysis of the reaction: ATP + tau-protein = ADP + O-phospho-tau-protein.
    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:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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:0003214    cardiac left ventricle morphogenesis    The process in which the left cardiac ventricle is generated and organized.
    GO:0032869    cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0036016    cellular response to interleukin-3    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 an interleukin-3 stimulus.
    GO:0099565    chemical synaptic transmission, postsynaptic    The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.
    GO:0007212    dopamine receptor signaling pathway    The series of molecular signals generated as a consequence of a dopamine receptor binding to one of its physiological ligands.
    GO:0097192    extrinsic apoptotic signaling pathway in absence of ligand    A series of molecular signals in which a signal is conveyed from the cell surface to trigger the apoptotic death of a cell. The pathway starts with withdrawal of a ligand from a cell surface receptor, and ends when the execution phase of apoptosis is triggered.
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0032007    negative regulation of TOR signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
    GO:0010905    negative regulation of UDP-glucose catabolic process    Any process that decreases the rate, frequency or extent of UDP-glucose catabolism. UDP-glucose catabolic processes are the chemical reactions and pathways resulting in the breakdown of UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0061052    negative regulation of cell growth involved in cardiac muscle cell development    Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state.
    GO:0046325    negative regulation of glucose import    Any process that stops, prevents, or reduces the frequency, rate or extent of the import of the hexose monosaccharide glucose into a cell or organelle.
    GO:2000466    negative regulation of glycogen (starch) synthase activity    Any process that stops, prevents or reduces the frequency, rate or extent of glycogen (starch) synthase activity.
    GO:0045719    negative regulation of glycogen biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:1904227    negative regulation of glycogen synthase activity, transferring glucose-1-phosphate    Any process that stops, prevents or reduces the frequency, rate or extent of glycogen synthase activity, transferring glucose-1-phosphate.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:2000077    negative regulation of type B pancreatic cell development    Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    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:0071879    positive regulation of adrenergic receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of the adrenergic receptor protein signaling pathway. An adrenergic receptor signaling pathway is the series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands.
    GO:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:2000467    positive regulation of glycogen (starch) synthase activity    Any process that activates or increases the frequency, rate or extent of glycogen (starch) synthase activity.
    GO:0045823    positive regulation of heart contraction    Any process that activates or increases the frequency, rate or extent of heart contraction.
    GO:1901030    positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
    GO:0003073    regulation of systemic arterial blood pressure    The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
cellular component
    GO:0030877    beta-catenin destruction complex    A cytoplasmic protein complex containing glycogen synthase kinase-3-beta (GSK-3-beta), the adenomatous polyposis coli protein (APC), and the scaffolding protein axin, among others; phosphorylates beta-catenin, targets it for degradation by the proteasome.
    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: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:0098794    postsynapse    The part of a synapse that is part of the post-synaptic cell.

 Visualization

(-) Interactive Views

Theoretical Model
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dfm)
 
  Sites
(no "Sites" information available for 2dfm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dfm)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2dfm
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GSK3A_HUMAN | P49840
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.1.37
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  GSK3A_HUMAN | P49840
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2DFM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2DFM)