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Yorodumi- PDB-8gwr: Near full length Kidney type Glutaminase in complex with 2,2-Dime... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gwr | ||||||
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Title | Near full length Kidney type Glutaminase in complex with 2,2-Dimethyl-2,3-Dihydrobenzo[a] Phenanthridin-4(1H)-one (DDP) | ||||||
Components | Glutaminase kidney isoform, mitochondrial | ||||||
Keywords | ONCOPROTEIN / Glutaminase / complex / allosteric inhibition / small molecule inhibitor / cancer | ||||||
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: 2.801 Å | ||||||
Authors | Shankar, S. / Jobichen, C. / Sivaraman, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Febs J. / Year: 2023 Title: A novel allosteric site employs a conserved inhibition mechanism in human kidney-type glutaminase. Authors: Shankar, S. / Ramachandran, S. / Tulsian, N. / Radhakrishnan, S. / Jobichen, C. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gwr.cif.gz | 205.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gwr.ent.gz | 161 KB | Display | PDB format |
PDBx/mmJSON format | 8gwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gwr_validation.pdf.gz | 881 KB | Display | wwPDB validaton report |
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Full document | 8gwr_full_validation.pdf.gz | 893.4 KB | Display | |
Data in XML | 8gwr_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 8gwr_validation.cif.gz | 49.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/8gwr ftp://data.pdbj.org/pub/pdb/validation_reports/gw/8gwr | HTTPS FTP |
-Related structure data
Related structure data | 3voyS 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
#1: Protein | Mass: 73553.992 Da / Num. of mol.: 2 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-HZO / | #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: 3.37 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.5M sodium malonate pH 7, 4% jeffamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 94454 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 31.47 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 3870 / Rsym value: 0.718 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VOY Resolution: 2.801→46.871 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.82 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→46.871 Å
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LS refinement shell |
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