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Yorodumi- PDB-8f5f: human branched chain ketoacid dehydrogenase kinase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f5f | ||||||
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Title | human branched chain ketoacid dehydrogenase kinase in complex with inhibitors | ||||||
Components | [3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial | ||||||
Keywords | SIGNALING PROTEIN / TRANSFERASE/INHIBITOR / branched chain ketoacid dehydrogenase kinase / inhibitor / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of cellular amino acid metabolic process / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / amino acid catabolic process / Branched-chain amino acid catabolism / lipid biosynthetic process / protein serine/threonine phosphatase activity ...negative regulation of cellular amino acid metabolic process / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / amino acid catabolic process / Branched-chain amino acid catabolism / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / kinase activity / non-specific serine/threonine protein kinase / mitochondrial matrix / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.149 Å | ||||||
Authors | Liu, S. / Roth Flach, R. / Bollinger, E. / Filipski, K. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels. Authors: Roth Flach, R.J. / Bollinger, E. / Reyes, A.R. / Laforest, B. / Kormos, B.L. / Liu, S. / Reese, M.R. / Martinez Alsina, L.A. / Buzon, L. / Zhang, Y. / Bechle, B. / Rosado, A. / Sahasrabudhe, ...Authors: Roth Flach, R.J. / Bollinger, E. / Reyes, A.R. / Laforest, B. / Kormos, B.L. / Liu, S. / Reese, M.R. / Martinez Alsina, L.A. / Buzon, L. / Zhang, Y. / Bechle, B. / Rosado, A. / Sahasrabudhe, P.V. / Knafels, J. / Bhattacharya, S.K. / Omoto, K. / Stansfield, J.C. / Hurley, L.D. / Song, L. / Luo, L. / Breitkopf, S.B. / Monetti, M. / Cunio, T. / Tierney, B. / Geoly, F.J. / Delmore, J. / Siddall, C.P. / Xue, L. / Yip, K.N. / Kalgutkar, A.S. / Miller, R.A. / Zhang, B.B. / Filipski, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f5f.cif.gz | 282.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5f.ent.gz | 231.2 KB | Display | PDB format |
PDBx/mmJSON format | 8f5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5f ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5f | HTTPS FTP |
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-Related structure data
Related structure data | 8f5jC 8f5sC 4e01S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44251.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCKDK / Production host: Escherichia coli (E. coli) References: UniProt: O14874, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase |
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-Non-polymers , 5 types, 21 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #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: 3.39 Å3/Da / Density % sol: 63.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate and 17-22% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.149→47.67 Å / Num. obs: 18569 / % possible obs: 93.3 % / Redundancy: 13.1 % / CC1/2: 1 / Rpim(I) all: 0.032 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 3.149→3.227 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 751 / CC1/2: 0.566 / Rpim(I) all: 0.586 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 40 / Resolution: 3.149→47.67 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.51
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Displacement parameters | Biso mean: 120.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.53 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.149→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.19 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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