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Yorodumi- PDB-7ebg: Crystal structure of human pyruvate dehydrogenase kinase 4 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ebg | ||||||
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Title | Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 7 | ||||||
Components | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial | ||||||
Keywords | TRANSFERASE / PDHK / KINASE INHIBITORS / FRAGMENT SCREENING / PDK1 / PDK2 / PDK3 / PDK4 | ||||||
Function / homology | Function and homology information [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / regulation of fatty acid oxidation / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of fatty acid biosynthetic process / regulation of cellular ketone metabolic process / regulation of pH / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of bone resorption / cellular response to fatty acid ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / regulation of fatty acid oxidation / pyruvate dehydrogenase (acetyl-transferring) kinase activity / regulation of fatty acid biosynthetic process / regulation of cellular ketone metabolic process / regulation of pH / Regulation of pyruvate dehydrogenase (PDH) complex / regulation of bone resorption / cellular response to fatty acid / Signaling by Retinoic Acid / response to starvation / negative regulation of anoikis / regulation of glucose metabolic process / cellular response to starvation / reactive oxygen species metabolic process / insulin receptor signaling pathway / glucose homeostasis / protein kinase activity / mitochondrial matrix / phosphorylation / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Orita, T. / Doi, S. / Iwanaga, T. / Adachi, T. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Authors: Akaki, T. / Bessho, Y. / Ito, T. / Fujioka, S. / Ubukata, M. / Mori, G. / Yamanaka, K. / Orita, T. / Doi, S. / Iwanaga, T. / Ikegashira, K. / Hantani, Y. / Nakanishi, I. / Adachi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ebg.cif.gz | 332.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ebg.ent.gz | 237.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ebg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ebg_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7ebg_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7ebg_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 7ebg_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/7ebg ftp://data.pdbj.org/pub/pdb/validation_reports/eb/7ebg | HTTPS FTP |
-Related structure data
Related structure data | 7ea0C 7easC 7eatC 7ebbC 7ebhC 2zkjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45598.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK4, PDHK4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q16654, [pyruvate dehydrogenase (acetyl-transferring)] kinase |
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-Non-polymers , 5 types, 180 molecules
#2: Chemical | #3: Chemical | ChemComp-J0L / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-ADP / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.34 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM KHPO4 pH 7.5, 1.7 M ammonium sulfate and 4% (v/v) PEG400, 5 mM ADP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→68.64 Å / Num. obs: 51337 / % possible obs: 98.1 % / Redundancy: 3 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.039 / Rrim(I) all: 0.069 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique obs: 3739 / CC1/2: 0.815 / Rpim(I) all: 0.251 / Rrim(I) all: 0.436 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zkj Resolution: 1.95→68.64 Å / SU ML: 0.2076 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1605 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→68.64 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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