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Yorodumi- PDB-5i94: Crystal structure of human glutaminase C in complex with the inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i94 | |||||||||
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Title | Crystal structure of human glutaminase C in complex with the inhibitor UPGL-00019 | |||||||||
Components | Glutaminase kidney isoform, mitochondrial | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / glutaminase C / inhibitor / 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 / MOLECULAR REPLACEMENT / Resolution: 2.983 Å | |||||||||
Authors | Huang, Q. / Cerione, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2016 Title: Design and evaluation of novel glutaminase inhibitors. Authors: McDermott, L.A. / Iyer, P. / Vernetti, L. / Rimer, S. / Sun, J. / Boby, M. / Yang, T. / Fioravanti, M. / O'Neill, J. / Wang, L. / Drakes, D. / Katt, W. / Huang, Q. / Cerione, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i94.cif.gz | 327.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i94.ent.gz | 264.2 KB | Display | PDB format |
PDBx/mmJSON format | 5i94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/5i94 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/5i94 | HTTPS FTP |
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-Related structure data
Related structure data | 5fi2SC 5fi6C 5fi7C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 59429.535 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 (E. coli) / References: UniProt: O94925, glutaminase #2: Chemical | |
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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: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10% PEG6000, LiCl, Tris-HCl, pH8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→50 Å / Num. obs: 47296 / % possible obs: 99.9 % / Redundancy: 3.6 % / Net I/σ(I): 11.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fi2 Resolution: 2.983→46.397 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.42
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.983→46.397 Å
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Refine LS restraints |
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LS refinement shell |
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