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Yorodumi- PDB-7m5z: Crystal Structure of the MerTK Kinase Domain in Complex with Inhi... -
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-Basic information
Entry | Database: PDB / ID: 7m5z | ||||||
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Title | Crystal Structure of the MerTK Kinase Domain in Complex with Inhibitor MIPS15692 | ||||||
Components | Tyrosine-protein kinase Mer | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / Kinase / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis ...negative regulation of leukocyte apoptotic process / negative regulation of lymphocyte activation / neutrophil clearance / natural killer cell differentiation / secretion by cell / negative regulation of cytokine production / vagina development / photoreceptor outer segment / phagocytosis / positive regulation of phagocytosis / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / establishment of localization in cell / Cell surface interactions at the vascular wall / receptor protein-tyrosine kinase / platelet activation / cell migration / cell-cell signaling / retina development in camera-type eye / nervous system development / spermatogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor complex / protein phosphorylation / extracellular space / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å | ||||||
Authors | Hermans, S.J. / Hancock, N.C. / Baell, J.B. / Parker, M.W. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2021 Title: Development of [ 18 F]MIPS15692, a radiotracer with in vitro proof-of-concept for the imaging of MER tyrosine kinase (MERTK) in neuroinflammatory disease. Authors: Wong, S.W. / Vivash, L. / Mudududdla, R. / Nguyen, N. / Hermans, S.J. / Shackleford, D.M. / Field, J. / Xue, L. / Aprico, A. / Hancock, N.C. / Haskali, M. / Stashko, M.A. / Frye, S.V. / ...Authors: Wong, S.W. / Vivash, L. / Mudududdla, R. / Nguyen, N. / Hermans, S.J. / Shackleford, D.M. / Field, J. / Xue, L. / Aprico, A. / Hancock, N.C. / Haskali, M. / Stashko, M.A. / Frye, S.V. / Wang, X. / Binder, M.D. / Ackermann, U. / Parker, M.W. / Kilpatrick, T.J. / Baell, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m5z.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m5z.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 7m5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7m5z_validation.pdf.gz | 825.4 KB | Display | wwPDB validaton report |
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Full document | 7m5z_full_validation.pdf.gz | 837.3 KB | Display | |
Data in XML | 7m5z_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7m5z_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/7m5z ftp://data.pdbj.org/pub/pdb/validation_reports/m5/7m5z | HTTPS FTP |
-Related structure data
Related structure data | 7ab0S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36001.488 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residues 570-864 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MERTK, MER / Production host: Escherichia coli (E. coli) References: UniProt: Q12866, receptor protein-tyrosine kinase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Bis-tris Propane pH 7.5, 2.2 M Sodium Chloride, and 0.15 M Magnesium Chloride Temp details: Room Temperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953731894493 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953731894493 Å / Relative weight: 1 |
Reflection | Resolution: 3.06→48.72 Å / Num. obs: 11670 / % possible obs: 91.4 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.055 / Rrim(I) all: 0.141 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.06→3.27 Å / Redundancy: 7 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2255 / CC1/2: 0.911 / Rpim(I) all: 0.292 / Rrim(I) all: 0.773 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7ab0 Resolution: 3.06→44.122 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.14 / 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: 3.06→44.122 Å
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Refine LS restraints |
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LS refinement shell |
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