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Yorodumi- PDB-5hl1: Crystal structure of glutaminase C in complex with inhibitor CB-839 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hl1 | |||||||||
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Title | Crystal structure of glutaminase C in complex with inhibitor CB-839 | |||||||||
Components | Glutaminase kidney isoform, mitochondrial | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / glutaminase / CB-839 / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system 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: 2.4 Å | |||||||||
Authors | Huang, Q. / Cerione, R.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Crystal structure of the clinically relevant glutaminase inhibitot CB-839 in complex with glutaminase C Authors: Huang, Q. / Katt, W.P. / McDermott, L.A. / Cerione, R.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hl1.cif.gz | 334.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hl1.ent.gz | 267.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hl1 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hl1 | HTTPS FTP |
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-Related structure data
Related structure data | 5d3oS S: Starting model for refinement |
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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: 59457.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Plasmid: pQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94925, glutaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10% PEG6000 / PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.63 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: 0.63 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 96364 / % possible obs: 99.9 % / Redundancy: 7.3 % / Net I/σ(I): 15.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D3O Resolution: 2.4→47.479 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.05 / Stereochemistry target values: ML
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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: 2.4→47.479 Å
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Refine LS restraints |
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LS refinement shell |
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