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- PDB-4mha: Crystal structure of the catalytic domain of the proto-oncogene t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mha | ||||||
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Title | Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC1817 | ||||||
![]() | Tyrosine-protein kinase Mer | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TYROSINE KINASE / ACUTE LYMPHOBLASTIC LEUKEMIA / RATIONAL STRUCTURE-BASED DRUG DESIGN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Mciver, A. / Stashko, M.A. / Deryckere, D. / Branchford, B.R. / Hunter, D. / Kireev, D.B. / Miley, D.B.M. / Norris-Drouin, J. / Stewart, W.M. ...Zhang, W. / Mciver, A. / Stashko, M.A. / Deryckere, D. / Branchford, B.R. / Hunter, D. / Kireev, D.B. / Miley, D.B.M. / Norris-Drouin, J. / Stewart, W.M. / Lee, M. / Sather, S. / Zhou, Y. / Dipaola, J.A. / Machius, M. / Janzen, W.P. / Earp, H.S. / Graham, D.K. / Frye, S. / Wang, X. | ||||||
![]() | ![]() Title: Discovery of Mer specific tyrosine kinase inhibitors for the treatment and prevention of thrombosis. Authors: Zhang, W. / McIver, A.L. / Stashko, M.A. / DeRyckere, D. / Branchford, B.R. / Hunter, D. / Kireev, D. / Miley, M.J. / Norris-Drouin, J. / Stewart, W.M. / Lee, M. / Sather, S. / Zhou, Y. / Di ...Authors: Zhang, W. / McIver, A.L. / Stashko, M.A. / DeRyckere, D. / Branchford, B.R. / Hunter, D. / Kireev, D. / Miley, M.J. / Norris-Drouin, J. / Stewart, W.M. / Lee, M. / Sather, S. / Zhou, Y. / Di Paola, J.A. / Machius, M. / Janzen, W.P. / Earp, H.S. / Graham, D.K. / Frye, S.V. / Wang, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 206.1 KB | Display | ![]() |
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PDB format | ![]() | 166.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mh7C ![]() 3tcpS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35889.434 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, UNP RESIDUES 570-864 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q12866, receptor protein-tyrosine kinase #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 32.5 mg/mL in 20 mM Tris pH 8.0, 500mM sodium chloride, 2mM beta-mercaptoethanol, incubated with inhibitor (2.5 mM final concentration) overnight, mixed 1:1 with crystallization ...Details: Protein: 32.5 mg/mL in 20 mM Tris pH 8.0, 500mM sodium chloride, 2mM beta-mercaptoethanol, incubated with inhibitor (2.5 mM final concentration) overnight, mixed 1:1 with crystallization solution (27-33% (v/v) Peg400, 200 mM magnesium chloride, 100 mM Tris pH 8.5), VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2012 |
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→40.07 Å / Num. all: 19608 / Num. obs: 19608 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.59→2.61 Å / Redundancy: 4 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2 / Num. unique all: 483 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3TCP Resolution: 2.59→40.066 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→40.066 Å
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Refine LS restraints |
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LS refinement shell |
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