+Open data
-Basic information
Entry | Database: PDB / ID: 7b30 | ||||||
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Title | MST3 in complex with compound G-5555 | ||||||
Components | Serine/threonine-protein kinase 24 | ||||||
Keywords | TRANSFERASE / kinase inhibitors / structure-based drug design / SIK2 inhibitor / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tesch, R. / Rak, M. / Joerger, A.C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b30.cif.gz | 143.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b30.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b30_validation.pdf.gz | 727.2 KB | Display | wwPDB validaton report |
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Full document | 7b30_full_validation.pdf.gz | 727.5 KB | Display | |
Data in XML | 7b30_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 7b30_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b30 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b30 | HTTPS FTP |
-Related structure data
Related structure data | 7b31C 7b32C 7b33C 7b34C 7b35C 7b36C 3zhpS S: Starting model for refinement C: citing same article (ref.) |
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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: 34559.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STK24, MST3, STK3 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-59T / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.74 % |
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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 and 0.5 mM TCEP. Reservoir: 10% PEG 6000, 0.1M HEPES pH 7.0. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å |
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: 2.1→39.64 Å / Num. obs: 20236 / % possible obs: 97 % / Redundancy: 6 % / Biso Wilson estimate: 38.68 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.03 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1341 / CC1/2: 0.881 / Rpim(I) all: 0.19 / % possible all: 79.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZHP Resolution: 2.1→39.64 Å / SU ML: 0.1967 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5467 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: 45.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.64 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 | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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