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Yorodumi- PDB-6umf: Crystal structure of human GAC in complex with inhibitor UPGL00012 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6umf | ||||||||||||
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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: 2.68 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 | 6umf.cif.gz | 778.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6umf.ent.gz | 540 KB | Display | PDB format |
PDBx/mmJSON format | 6umf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6umf_validation.pdf.gz | 378.4 KB | Display | wwPDB validaton report |
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Full document | 6umf_full_validation.pdf.gz | 359.6 KB | Display | |
Data in XML | 6umf_validation.xml.gz | 1.9 KB | Display | |
Data in CIF | 6umf_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/6umf ftp://data.pdbj.org/pub/pdb/validation_reports/um/6umf | HTTPS FTP |
-Related structure data
Related structure data | 6ujgC 6ul9C 6umcC 6umdC 6umeC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 137 - 544 / Label seq-ID: 66 - 473
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-Components
#1: Protein | Mass: 58023.996 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 | #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: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 12% PEG6000, 1.0 M LiCl, pH 8.0 / 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: 2.68→50 Å / Num. obs: 63034 / % possible obs: 93.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 46.77 Å2 / Rsym value: 0.237 / Net I/σ(I): 4.08 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 0.45 / Num. unique obs: 2581 / CC1/2: 0.645 / Rsym value: 0.684 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3O Resolution: 2.68→48.64 Å / SU ML: 0.389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3171
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→48.64 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: -7.35057179115 Å / Origin y: -34.2949030442 Å / Origin z: 43.7997290656 Å
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Refinement TLS group | Selection details: all |