[English] 日本語
Yorodumi- PDB-5mrd: Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mrd | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket | ||||||||||||
Components | 3-phosphoinositide-dependent protein kinase 1 | ||||||||||||
Keywords | TRANSFERASE / Protein Kinase / Allosteric Regulation / Small Compounds / PIF-pocket | ||||||||||||
Function / homology | Function and homology information 3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / negative regulation of cardiac muscle cell apoptotic process ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / negative regulation of cardiac muscle cell apoptotic process / positive regulation of vascular endothelial cell proliferation / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / GPVI-mediated activation cascade / cellular response to epidermal growth factor stimulus / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / cell migration / Regulation of TP53 Degradation / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | ||||||||||||
Authors | Arencibia, J.M. / Froehner, W. / Krupa, M. / Pastor-Flores, D. / Merker, P. / Oellerich, T. / Neimanis, S. / Schmithals, C. / Koeberle, V. / Suess, E. ...Arencibia, J.M. / Froehner, W. / Krupa, M. / Pastor-Flores, D. / Merker, P. / Oellerich, T. / Neimanis, S. / Schmithals, C. / Koeberle, V. / Suess, E. / Zeuzem, S. / Stark, H. / Piiper, A. / Odadzic, D. / Schulze, J.O. / Biondi, R.M. | ||||||||||||
Funding support | Germany, 3items
| ||||||||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: An Allosteric Inhibitor Scaffold Targeting the PIF-Pocket of Atypical Protein Kinase C Isoforms. Authors: Arencibia, J.M. / Frohner, W. / Krupa, M. / Pastor-Flores, D. / Merker, P. / Oellerich, T. / Neimanis, S. / Schmithals, C. / Koberle, V. / Su, E. / Zeuzem, S. / Stark, H. / Piiper, A. / ...Authors: Arencibia, J.M. / Frohner, W. / Krupa, M. / Pastor-Flores, D. / Merker, P. / Oellerich, T. / Neimanis, S. / Schmithals, C. / Koberle, V. / Su, E. / Zeuzem, S. / Stark, H. / Piiper, A. / Odadzic, D. / Schulze, J.O. / Biondi, R.M. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5mrd.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5mrd.ent.gz | 154.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mrd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrd ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrd | HTTPS FTP |
---|
-Related structure data
Related structure data | 3hrcS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35281.379 Da / Num. of mol.: 1 Mutation: K76S, L113V, I118V, I119N, V124I, T128Q, R131K, T148C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O15530, non-specific serine/threonine protein kinase |
---|
-Non-polymers , 5 types, 334 molecules
#2: Chemical | ChemComp-S26 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-DTT / | ||||
#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 10 MM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→47 Å / Num. obs: 57639 / % possible obs: 97.1 % / Redundancy: 2.5 % / Net I/σ(I): 13 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HRC Resolution: 1.41→46.772 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.61
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→46.772 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|