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Yorodumi- PDB-6ujg: Crystal structure of human GAC in complex with inhibitor UPGL00012 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ujg | ||||||||||||
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Title | Crystal structure of human GAC in complex with inhibitor UPGL00012 | ||||||||||||
Components | Glutaminase kidney isoform, mitochondrial | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Complex / HYDROLASE / 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: 3 Å | ||||||||||||
Authors | Huang, Q. / Cerione, R.A. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structure of human GAC in complex with inhibitor UPGL00012 Authors: Huang, Q. / Cerione, R.A. #1: Journal: J. Biol. Chem. / Year: 2018 Title: Characterization of the interactions of potent allosteric inhibitors with glutaminase C, a key enzyme in cancer cell glutamine metabolism. Authors: Huang, Q. / Stalnecker, C.A. / Zhang, C. / McDermott, L.A. / Iyer, P. / O'Neill, J. / Reimer, S. / Cerione, R.A. / Katt, W.P. #2: Journal: Bioorg. Med. Chem. / Year: 2016 Title: Design and evaluation of novel glutaminase inhibitors. Authors: McDermott, L.A. / Iyer, P. / Vernetti, L. / Reimer, S. / Sun, J. / Boby, M. / Yang, T. / Fioravanti, M. / O'Neill, J. / Wang, L. / Drakes, D. / Katt, W.P. / Huang, Q. / Cerione, R.A. #3: Journal: J. Biol. Chem. / Year: 2016 Title: Mechanistic Basis of Glutaminase Activation: A KEY ENZYME THAT PROMOTES GLUTAMINE METABOLISM IN CANCER CELLS. Authors: Li, Y. / Erickson, J.W. / Stalnecker, C.A. / Katt, W.P. / Huang, Q. / Cerione, R.A. / Ramachandran, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ujg.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ujg.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6ujg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ujg_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6ujg_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6ujg_validation.xml.gz | 111.2 KB | Display | |
Data in CIF | 6ujg_validation.cif.gz | 151.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6ujg ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6ujg | HTTPS FTP |
-Related structure data
Related structure data | 6ul9C 6umcC 6umdC 6umeC 6umfC 5d3oS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58023.996 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O94925, glutaminase #2: Chemical | ChemComp-Q9A / 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: 3.33 Å3/Da / Density % sol: 63.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% PEG6000, 1.0M LiCl, pH8.0 / PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 105300 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.51 Å2 / CC1/2: 0.573 / Rrim(I) all: 0.293 / Rsym value: 0.188 / Net I/σ(I): 6.39 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 0.982 / Num. unique obs: 5072 / Rsym value: 0.768 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3O Resolution: 3→34.94 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.7842
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→34.94 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.33421929934 Å / Origin y: -36.3803322488 Å / Origin z: 44.3068462356 Å
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Refinement TLS group | Selection details: all |