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Yorodumi- PDB-3vp4: Crystal structure of human glutaminase in complex with inhibitor 4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vp4 | ||||||
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Title | Crystal structure of human glutaminase in complex with inhibitor 4 | ||||||
Components | Glutaminase kidney isoform, mitochondrial | ||||||
Keywords | HYDROLASE/HYDROLASE 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: 2.45 Å | ||||||
Authors | Thangavelu, K. / Sivaraman, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis for the allosteric inhibitory mechanism of human kidney-type glutaminase (KGA) and its regulation by Raf-Mek-Erk signaling in cancer cell metabolism. Authors: Thangavelu, K. / Pan, C.Q. / Karlberg, T. / Balaji, G. / Uttamchandani, M. / Suresh, V. / Schuler, H. / Low, B.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 | 3vp4.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vp4.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vp4_validation.pdf.gz | 734.4 KB | Display | wwPDB validaton report |
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Full document | 3vp4_full_validation.pdf.gz | 738.3 KB | Display | |
Data in XML | 3vp4_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3vp4_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/3vp4 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/3vp4 | HTTPS FTP |
-Related structure data
Related structure data | 3czdSC 3voyC 3vozC 3vp0C 3vp1C 3vp2C 3vp3C C: citing same article (ref.) 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: 34816.742 Da / Num. of mol.: 1 / Fragment: UNP Residues 221-533 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 |
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#2: Chemical | ChemComp-BP9 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.65M Lithium sulfate, 100mM Bis-tris-propane pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 28767 / % possible obs: 99.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CZD Resolution: 2.45→30 Å
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Refinement step | Cycle: LAST / Resolution: 2.45→30 Å
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