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Yorodumi- PDB-2coa: Solution structure of the PH domain of protein kinase C, D2 type ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2coa | ||||||
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Title | Solution structure of the PH domain of protein kinase C, D2 type from human | ||||||
Components | Protein kinase C, D2 type | ||||||
Keywords | SIGNALING PROTEIN / Protein kinase D2 / PH domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information protein kinase C / positive regulation of fibroblast growth factor receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / endothelial tube morphogenesis / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / regulation of T cell apoptotic process / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial growth factor receptor signaling pathway ...protein kinase C / positive regulation of fibroblast growth factor receptor signaling pathway / diacylglycerol-dependent serine/threonine kinase activity / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / endothelial tube morphogenesis / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / regulation of T cell apoptotic process / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of intracellular signal transduction / positive regulation of DNA biosynthetic process / positive regulation of T cell receptor signaling pathway / positive regulation of cell adhesion / cellular response to vascular endothelial growth factor stimulus / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of interleukin-2 production / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / protein kinase C binding / positive regulation of interleukin-8 production / peptidyl-threonine phosphorylation / positive regulation of DNA-binding transcription factor activity / positive regulation of angiogenesis / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / peptidyl-serine phosphorylation / angiogenesis / protein autophosphorylation / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / cell adhesion / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PH domain of protein kinase C, D2 type from human Authors: Li, H. / Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2coa.cif.gz | 727.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2coa.ent.gz | 607.8 KB | Display | PDB format |
PDBx/mmJSON format | 2coa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/2coa ftp://data.pdbj.org/pub/pdb/validation_reports/co/2coa | HTTPS FTP |
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-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: 13583.098 Da / Num. of mol.: 1 / Fragment: PH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PKD2 / Plasmid: P041129-04 References: UniProt: Q9BZL6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.38mM PH domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-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: target function,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |