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(-) Description

Title :  STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 1
 
Authors :  M. Kato, J. Li, J. L. Chuang, D. T. Chuang
Date :  10 Jun 07  (Deposition) - 24 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ghkl Atpase/Kinase Family, Pyruvate Dehydrogenase Complex, Mitochondrial Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kato, J. Li, J. L. Chuang, D. T. Chuang
Distinct Structural Mechanisms For Inhibition Of Pyruvate Dehydrogenase Kinase Isoforms By Azd7545, Dichloroacetate, And Radicicol.
Structure V. 15 992 2007
PubMed-ID: 17683942  |  Reference-DOI: 10.1016/J.STR.2007.07.001

(-) Compounds

Molecule 1 - [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1
    ChainsA
    EC Number2.7.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GenePDK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPYRUVATE DEHYDROGENASE KINASE ISOFORM 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:50 , ARG A:51 , PHE A:52 , ASN A:89 , VAL A:402 , TYR A:403 , HOH A:510BINDING SITE FOR RESIDUE K A 437

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q8F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q8F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050477A134TPDK1_HUMANPolymorphism35661499AA134T
2UniProtVAR_042295N412TPDK1_HUMANPolymorphism34250425AN412T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050477A134TPDK1_HUMANPolymorphism35661499AA134T
2UniProtVAR_042295N412TPDK1_HUMANPolymorphism34250425AN412T

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q8F)

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002820772aENSE00001930036chr2:173420697-173421074378PDK1_HUMAN1-66661A:41-6626
1.4ENST000002820774ENSE00001704322chr2:173423436-173423577142PDK1_HUMAN66-113481A:66-113 (gaps)48
1.5ENST000002820775ENSE00001171998chr2:173426948-17342701972PDK1_HUMAN113-137251A:113-13725
1.8ENST000002820778ENSE00001593149chr2:173429231-173429415185PDK1_HUMAN137-199631A:137-199 (gaps)63
1.9ENST000002820779ENSE00002165646chr2:173429706-17342980196PDK1_HUMAN199-231331A:199-231 (gaps)33
1.10ENST0000028207710ENSE00001639357chr2:173431584-17343166178PDK1_HUMAN231-257271A:231-25727
1.11ENST0000028207711ENSE00001004281chr2:173433469-17343354577PDK1_HUMAN257-282261A:257-28226
1.12dENST0000028207712dENSE00001004287chr2:173435454-17343555299PDK1_HUMAN283-315331A:283-31533
1.13ENST0000028207713ENSE00001171959chr2:173451006-173451116111PDK1_HUMAN316-352371A:316-35237
1.14ENST0000028207714ENSE00001171952chr2:173457663-173457776114PDK1_HUMAN353-390381A:353-39038
1.15dENST0000028207715dENSE00001341369chr2:173460557-173461193637PDK1_HUMAN391-436461A:391-423 (gaps)33

(-) Sequences/Alignments

Asymmetric 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:365
 aligned with PDK1_HUMAN | Q15118 from UniProtKB/Swiss-Prot  Length:436

    Alignment length:383
                                    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       360       370       380       390       400       410       420   
           PDK1_HUMAN    41 GVPGQVDFYARFSPSPLSMKQFLDFGSVNACEKTSFMFLRQELPVRLANIMKEISLLPDNLLRTPSVQLVQSWYIQSLQELLDFKDKSAEDAKAIYDFTDTVIRIRNRHNDVIPTMAQGVIEYKESFGVDPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFGGKGKGSPSHRKHIGSINPNCNVLEVIKDGYENARRLCDLYYINSPELELEELNAKSPGQPIQVVYVPSHLYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDRLFNYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQYFQGDLKLYSLEGYGTDAVIYIKALSTDSIERLPVYNKAAWKHYNTNHEADDWCVP 423
               SCOP domains d2q8fa1 A:41-202 automated    matches                                                                                                                             -           d2q8fa2 A:215-423 automated matches                                                                                                                                                                               SCOP domains
               CATH domains 2q8fA01 A:41-203  [code=1.2   0.140.20, no name defined]                                                                                                                      2q8fA02 A:215-399  [code=3.30.565.10, no name defined]                                                                                                                                   ---------------  ------- CATH domains
               Pfam domains --------------BCDHK_Adom3-2   q8fA02 A:55-221                                                                                                                                        ----------------------------------------------HATPase_c-2q8fA01 A:268-392                                                                                                  ----------------------  ------- Pfam domains
         Sec.struct. author hhhhhhhhhhh......hhhhhhhhhh---hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh--.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------.....eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhhh.......................hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.............hhhhhhhhh..--....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T----------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:41-66   ----------------------------------------------Exon 1.5  PDB: A:113-137 ---------------------------------------------------------------------------------------------Exon 1.10  PDB: A:231-257  -------------------------Exon 1.12d  PDB: A:283-315       Exon 1.13  PDB: A:316-352            Exon 1.14  PDB: A:353-390             Exon 1.15d  PDB: A:391-423 (gaps) Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.4  PDB: A:66-113 (gaps) UniProt: 66-113  -----------------------Exon 1.8  PDB: A:137-199 (gaps) UniProt: 137-199               ---------------------------------------------------------Exon 1.11  PDB: A:257-282 --------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:199-231 (gaps)  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (3)
                 2q8f A  41 GVPGQVDFYARFSPSPLSMKQFLDFGS---CEKTSFMFLRQELPVRLANIMKEISLLPDNLLRTPSVQLVQSWYIQSLQELLDFKDKSAEDAKAIYDFTDTVIRIRNRHNDVIPTMAQGVIEYKESF--DPVTSQNVQYFLDRFYMSRISIRMLLNQHSLLFG-----------HIGSINPNCNVLEVIKDGYENARRLCDLYYINSPELELEELNAKSPGQPIQVVYVPSHLYHMVFELFKNAMRATMEHHANRGVYPPIQVHVTLGNEDLTVKMSDRGGGVPLRKIDRLFNYMYSTAPRPRVETSRAVPLAGFGYGLPISRLYAQYFQGDLKLYSLEGYGTDAVIYIKALSTDSIERLPVYNKAAWKHYNTN--ADDWCVP 423
                                    50        60      |  -|       80        90       100       110       120       130       140       150       160      |170       180       190       200  |      -    |  220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410   |  |420   
                                                     67  71                                                                                             167  |                              203         215                                                                                                                                                                                                    414  |      
                                                                                                                                                           170                                                                                                                                                                                                                                                    417      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (PDK1_HUMAN | Q15118)
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: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:0004740    pyruvate dehydrogenase (acetyl-transferring) kinase activity    Catalysis of the reaction: ATP + pyruvate dehydrogenase (acetyl-transferring) = ADP + pyruvate dehydrogenase (acetyl-transferring) 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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0006006    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.
    GO:0097411    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.
    GO:0008631    intrinsic apoptotic signaling pathway in response to oxidative stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered.
    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:0098779    positive regulation of macromitophagy in response to mitochondrial depolarization    The macromitophagy process that is triggered by a detection of the loss of mitochondrial membrane potential.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0010510    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.
    GO:0010906    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.
cellular component
    GO:0005759    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.
    GO:0005967    mitochondrial pyruvate dehydrogenase complex    Complex that carries out the oxidative decarboxylation of pyruvate to form acetyl-CoA in eukaryotes; includes subunits possessing three catalytic activities: pyruvate dehydrogenase (E1), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). The This Eukaryotic form usually contains more subunits than its bacterial counterpart; for example, one known complex contains 30 E1 dimers, 60 E2 monomers, and 6 E3 dimers as well as a few copies of pyruvate dehydrogenase kinase and pyruvate dehydrogenase phosphatase.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDK1_HUMAN | Q151182q8g 2q8h

(-) Related Entries Specified in the PDB File

2q8g PDK1-AZD7545 COMPLEX
2q8h PDK1-DCA COMPLEX
2q8i PDK3-RADICICOL COMPLEX