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Yorodumi- PDB-8f4q: rat branched chain ketoacid dehydrogenase kinase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f4q | ||||||
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Title | rat branched chain ketoacid dehydrogenase kinase in complex with inhibtors | ||||||
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 [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / lipid biosynthetic process ...[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase / [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity / : / Branched-chain amino acid catabolism / L-leucine catabolic process / valine catabolic process / isoleucine catabolic process / pyruvate dehydrogenase (acetyl-transferring) kinase activity / branched-chain amino acid catabolic process / lipid biosynthetic process / protein serine/threonine phosphatase activity / regulation of glucose metabolic process / spermatogenesis / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | Rattus (rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å | ||||||
Authors | Liu, S. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Discovery of branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors acting as stabilizers or destabilizers Authors: Roth Flach, R. / Filipski, K. / Bollinger, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f4q.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f4q.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f4/8f4q ftp://data.pdbj.org/pub/pdb/validation_reports/f4/8f4q | HTTPS FTP |
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-Related structure data
Related structure data | 4e00S S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | [ Mass: 44261.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat) / Gene: Bckdk / Production host: Escherichia coli (E. coli) References: UniProt: Q00972, [3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase | ||||||
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#2: Chemical | ChemComp-ADP / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MES pH 5.4, 0.2 M magnesium chloride, and 10% 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 R 4M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→92.7 Å / Num. obs: 22708 / % possible obs: 88 % / Redundancy: 18.6 % / CC1/2: 1 / Rpim(I) all: 0.017 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.154→2.305 Å / Num. unique obs: 1136 / CC1/2: 0.602 / Rpim(I) all: 0.611 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 4 / Resolution: 2.151→23.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.262 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.215
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Displacement parameters | Biso mean: 80.02 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.151→23.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.27 Å
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Refinement TLS params. | Origin x: 101.7881 Å / Origin y: 36.0858 Å / Origin z: 22.7462 Å
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Refinement TLS group |
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