+Open data
-Basic information
Entry | Database: PDB / ID: 4qml | ||||||
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Title | MST3 in complex with AMP-PNP | ||||||
Components | Serine/threonine-protein kinase 24Serine/threonine-specific protein kinase | ||||||
Keywords | Transferase/transferase inhibitor / PROTEIN KINASE / MST3 / STK24 / STERILE 20-LIKE KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / SERINE/THREONINE-TRANSFERASE / Transferase-transferase inhibitor complex | ||||||
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 / response to hydrogen peroxide / 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 / response to hydrogen peroxide / 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 / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.882 Å | ||||||
Authors | Olesen, S.H. / Watts, C. / Zhu, J.-Y. / Schonbrunn, E. | ||||||
Citation | Journal: Chemmedchem / Year: 2016 Title: Discovery of Diverse Small-Molecule Inhibitors of Mammalian Sterile20-like Kinase 3 (MST3). Authors: Olesen, S.H. / Zhu, J.Y. / Martin, M.P. / Schonbrunn, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qml.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qml.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 4qml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/4qml ftp://data.pdbj.org/pub/pdb/validation_reports/qm/4qml | HTTPS FTP |
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-Related structure data
Related structure data | 4qmmC 4qmnC 4qmoC 4qmpC 4qmqC 4qmsC 4qmtC 4qmuC 4qmvC 4qmwC 4qmxC 4qmyC 4qmzC 4qnaC 4qo9C 3ckwS 4qmr C: citing same article (ref.) S: Starting model for refinement |
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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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Details | one molecule per ASU |
-Components
#1: Protein | Mass: 35023.934 Da / Num. of mol.: 1 / Fragment: unp residues 1-303 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MST3, STK24, STK3 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL References: UniProt: Q9Y6E0, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ANP / |
#5: Water | ChemComp-HOH / |
Sequence details | THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.5 mg/mL MST3, 1 mM ANP-PNP, 25 mM TRIS, PH 8.0, 50 MM HEPES pH 7.5, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 / Wavelength: 1.54 Å | |||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 29, 2012 / Details: MIRRORS | |||||||||
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.88→20 Å / Num. obs: 23571 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.035 / Net I/σ(I): 44.1 | |||||||||
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.288 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3CKW Resolution: 1.882→39.343 Å / SU ML: 0.18 / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.882→39.343 Å
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Refine LS restraints |
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LS refinement shell |
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