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An Information Portal to 105097 Biological Macromolecular Structures

Crystal structure of the PDK3-L2 complex
Biology and Chemistry Report
1Y8O
  •   Structure Details   Hide

    Structure Keywords

    Keywords transferase
    Text pyruvate dehydrogenase kinase 3, lipoyl-bearing domain, protein-protein complex, transferase

    Polymeric Molecules

    Chain A
    Description [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 48291.5 
    Source Method genetically manipulated  
    Entity Name Pyruvate dehydrogenase kinase isoform 3 
    Chain B
    Description Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 14192.2 
    Source Method genetically manipulated  
    Entity Name E2, Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, PDC-E2, 70 kDa mitochondrial autoantigen of primary biliary cirrhosis, PBC, M2 antigen complex 70 kDa subunit 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ADP  ADENOSINE-5'-DIPHOSPHATE  C10 H15 N5 O10 P2   427.20  View 
    POTASSIUM ION  K   39.10  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    RED  DIHYDROLIPOIC ACID  C8 H16 O2 S2   208.34  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A PDK3_HUMAN B4DXG6     
    B ODP2_HUMAN P10515     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    2.7.11.2        
    2.3.1.12        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    5975   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. 
    6006   Glucose Metabolic Process  The Chemical Reactions and Pathways Involving Glucose the Aldohexose Gluco Hexose. D Glucose Is Dextrorotatory and Is Sometimes Known As Dextrose; It Is an Important Source of Energy For Living Organisms and Is Found Free As Well As Combined in Homo and Hetero Oligosaccharides and Polysaccharides. 
    6090   Pyruvate Metabolic Process  The Chemical Reactions and Pathways Involving Pyruvate 2 Oxopropanoate. 
    10510   Regulation of Acetyl Coa Biosynthetic Process From Pyruvate  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Acetyl Coa From Pyruvate. 
    10906   Regulation of Glucose Metabolic Process  Any Process That Modulates the Rate Frequency or Extent of Glucose Metabolism. Glucose Metabolic Processes Are the Chemical Reactions and Pathways Involving Glucose the Aldohexose Gluco Hexose. 
    16310   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. 
    18105   Peptidyl Serine Phosphorylation  The Phosphorylation of Peptidyl Serine to Form Peptidyl O Phospho L Serine. 
    35357   Peroxisome Proliferator Activated Receptor Signaling Pathway  The Series of Molecular Signals Initiated by Binding of a Ligand to Any of the Peroxisome Proliferator Activated Receptors (alpha Beta or Gamma) in the Nuclear Membrane and Ending with the Initiation or Termination of the Transcription of Target Genes. 
    44237   Cellular Metabolic Process  The Chemical Reactions and Pathways by Which Individual Cells Transform Chemical Substances. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    71333   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. 
    71398   Cellular Response to Fatty Acid  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 Fatty Acid Stimulus. 
    97411   Hypoxia Inducible Factor 1alpha Signaling Pathway  A Series of Molecular Signals Mediated by Hypoxia Inducible Factor (hif1) in Response to Lowered Oxygen Levels (hypoxia). Under Hypoxic Conditions the Oxygen Sensitive Alpha Subunit of Hypoxia Inducible Factor (hif) 1 Dimerizes with a Hif1 Beta Subunit (also Called Arnt or Aryl Hydrocarbon Receptor Nuclear Translocator) Translocates to the Nucleus and Activates Transcription of Genes Whose Products Participate in Responding to Hypoxia. 
    2000377   Regulation of Reactive Oxygen Species Metabolic Process  Any Process That Modulates the Frequency Rate or Extent of Reactive Oxygen Species Metabolic Process. 
    5739   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. 
    5759   Mitochondrial Matrix  The Gel Like Material with Considerable Fine Structure That Lies in the Matrix Space or Lumen of a Mitochondrion. It Contains the Enzymes of the Tricarboxylic Acid Cycle and in Some Organisms the Enzymes Concerned with Fatty Acid Oxidation. 
    166   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. 
    4672   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. 
    4674   Protein Serine/threonine Kinase Activity  Catalysis of the Reactions: ATP + Protein Serine = Adp + Protein Serine Phosphate and ATP + Protein Threonine = Adp + Protein Threonine Phosphate. 
    4740   Pyruvate Dehydrogenase (acetyl Transferring) Kinase Activity  Catalysis of the Reaction: ATP + Pyruvate Dehydrogenase (acetyl Transferring) = Adp + Pyruvate Dehydrogenase (acetyl Transferring) Phosphate. 
    5515   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). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene dlat, dlta
    Host Scientific Name Escherichia coli bl21  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21
    Host Vector Type Plasmid
    Host Plasmid Name pTrcHisB


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene pdk3
    Host Scientific Name Escherichia coli bl21  
    Host Genus Escherichia
    Host Species Escherichia Coli
    Host Strain Bl21
    Host Vector Type Plasmid
    Host Plasmid Name pTrcHisB


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q23.1 1737     dihydrolipoamide S-acetyltransferase DLAT    
    X Xp22.11 5165     pyruvate dehydrogenase kinase, isozyme 3 PDK3    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs112864206 LS-SNP   dbSNP   A 66 L - > I Turn 21% (Intermediate) X 24512948
    rs146331370 LS-SNP   dbSNP   A 114 K - > T Helix 54% (Exposed) X 24521464
    rs138321172 LS-SNP   dbSNP   A 126 M - > V Helix 1% (Buried) X 24521499
    rs149603823 LS-SNP   dbSNP   A 175 D - > N Coil 63% (Exposed) X 24523343
    rs200598034 LS-SNP   dbSNP   A 224 N - > S Beta Ladder 8% (Buried) X 24537125
    rs5986591 LS-SNP   dbSNP   A 336 R - > K Helix 24% (Intermediate) X 24549817
    rs199753392 LS-SNP   dbSNP   B 204 L - > V Beta Ladder 1% (Buried) 11 111908077
    rs11553592 LS-SNP   dbSNP   B 227 D - > V Coil 53% (Exposed) 11 111908147