+Open data
-Basic information
Entry | Database: PDB / ID: 8jub | ||||||
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Title | Crystal structure of glutaminase C in complex with compound 27 | ||||||
Components | Glutaminase kidney isoform, mitochondrial | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Complex / ANTITUMOR PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å | ||||||
Authors | Wang, X. / Hanyu, S. / Tingting, D. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 Title: Targeting the Subpocket Enables the Discovery of Thiadiazole-Pyridazine Derivatives as Glutaminase C Inhibitors. Authors: Sun, H. / Du, T. / Yang, M. / Liu, X. / Xue, X. / Chen, K. / Lang, X. / Chen, X. / Wang, B. / Wang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jub.cif.gz | 328.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jub.ent.gz | 261.2 KB | Display | PDB format |
PDBx/mmJSON format | 8jub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/8jub ftp://data.pdbj.org/pub/pdb/validation_reports/ju/8jub | HTTPS FTP |
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-Related structure data
Related structure data | 8jueC 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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Unit cell |
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-Components
#1: Protein | Mass: 58780.859 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94925, glutaminase #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.6 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% Polyethylene glycol 3350, 0.2 M magnesium chloride, 0.08 M 2-[4-(2-Hydroxyethyl)-1-piperazinyl]ethanesulfonicacid pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 10, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→89.24 Å / Num. obs: 145402 / % possible obs: 91.18 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07234 / Rpim(I) all: 0.03351 / Rrim(I) all: 0.07993 / Net I/σ(I): 15.72 |
Reflection shell | Resolution: 2.01→2.082 Å / Rmerge(I) obs: 0.6913 / Num. unique obs: 11575 / CC1/2: 0.708 / Rpim(I) all: 0.3733 / Rrim(I) all: 0.789 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.01→89.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.393 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.943 Å2
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Refinement step | Cycle: 1 / Resolution: 2.01→89.24 Å
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Refine LS restraints |
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