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Yorodumi- PDB-1r79: Solution Structure of The C1 Domain of The Human Diacylglycerol K... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r79 | ||||||
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Title | Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta | ||||||
Components | Diacylglycerol kinase, delta | ||||||
Keywords | TRANSFERASE / C1 Domain / Cystein-rich Zinc Binding Domain / Diacylglycerol Kinase Delta / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / : ...negative regulation of protein kinase C signaling / lipid phosphorylation / diacylglycerol metabolic process / diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / positive regulation of clathrin-dependent endocytosis / phosphatidic acid biosynthetic process / diacylglycerol binding / Effects of PIP2 hydrolysis / : / positive regulation of epidermal growth factor receptor signaling pathway / clathrin-coated pit / kinase binding / platelet activation / endocytosis / protein transport / cytoplasmic vesicle / intracellular signal transduction / protein heterodimerization activity / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution Structure of The C1 Domain of The Human Diacylglycerol Kinase Delta Authors: Miyamoto, K. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r79.cif.gz | 477.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r79.ent.gz | 396 KB | Display | PDB format |
PDBx/mmJSON format | 1r79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r79_validation.pdf.gz | 343.6 KB | Display | wwPDB validaton report |
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Full document | 1r79_full_validation.pdf.gz | 482.2 KB | Display | |
Data in XML | 1r79_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1r79_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/1r79 ftp://data.pdbj.org/pub/pdb/validation_reports/r7/1r79 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8826.108 Da / Num. of mol.: 1 / Fragment: C1 Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA ha00914 / Plasmid: P030128-49 / References: UniProt: Q16760, diacylglycerol kinase (ATP) |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.05mM C1 Domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.5); 100mM NaCl; 0.02% NaN3; 100uM ZnCl2; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |