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Open data
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Basic information
Entry | Database: PDB / ID: 7b32 | ||||||
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Title | MST3 in complex with MRIA7 | ||||||
![]() | Serine/threonine-protein kinase 24 | ||||||
![]() | TRANSFERASE / kinase inhibitors / structure-based drug design / SIK2 inhibitor / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation ...Apoptotic execution phase / regulation of axon regeneration / execution phase of apoptosis / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of axon regeneration / Apoptotic cleavage of cellular proteins / cellular response to starvation / negative regulation of cell migration / cellular response to oxidative stress / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleolus / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tesch, R. / Rak, M. / Joerger, A.C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Based Design of Selective Salt-Inducible Kinase Inhibitors. Authors: Tesch, R. / Rak, M. / Raab, M. / Berger, L.M. / Kronenberger, T. / Joerger, A.C. / Berger, B.T. / Abdi, I. / Hanke, T. / Poso, A. / Strebhardt, K. / Sanhaji, M. / Knapp, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.7 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 713.5 KB | Display | ![]() |
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Full document | ![]() | 714.3 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b30C ![]() 7b31C ![]() 7b33C ![]() 7b34C ![]() 7b35C ![]() 7b36C ![]() 3zhpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34559.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-SQQ / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein solution: 10 mg/ml in buffer 25 mM HEPES pH 7.5, 200 mM NaCl, 5% glycerol, 0.5mM TCEP. Reservoir: 20% PEG 3350, 0.1M bis-tris pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→49.9 Å / Num. obs: 36097 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.77 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1989 / CC1/2: 0.905 / Rpim(I) all: 0.209 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZHP Resolution: 1.75→49.9 Å / SU ML: 0.1713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3638 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→49.9 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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