+Open data
-Basic information
Entry | Database: PDB / ID: 7oam | ||||||
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Title | Kinase domain of MERTK in complex with compound 8 | ||||||
Components | Tyrosine-protein kinase Mer | ||||||
Keywords | TRANSFERASE / MERTK / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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 / 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 / receptor complex / cell surface receptor signaling pathway / 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: 2.65 Å | ||||||
Authors | Schroeder, M. / Russ, N. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Design and Development of a Chemical Probe for Pseudokinase Ca 2+ /calmodulin-Dependent Ser/Thr Kinase. Authors: Russ, N. / Schroder, M. / Berger, B.T. / Mandel, S. / Aydogan, Y. / Mauer, S. / Pohl, C. / Drewry, D.H. / Chaikuad, A. / Muller, S. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oam.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oam.ent.gz | 167.6 KB | Display | PDB format |
PDBx/mmJSON format | 7oam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oam_validation.pdf.gz | 704.3 KB | Display | wwPDB validaton report |
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Full document | 7oam_full_validation.pdf.gz | 707.4 KB | Display | |
Data in XML | 7oam_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 7oam_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/7oam ftp://data.pdbj.org/pub/pdb/validation_reports/oa/7oam | HTTPS FTP |
-Related structure data
Related structure data | 7oaiC 7oajC 7oakC 7oalC 4m3qS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Label seq-ID: 8 - 294
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-Components
#1: Protein | Mass: 34074.504 Da / Num. of mol.: 2 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: Chemical | ChemComp-V6H / | #4: 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: 2.36 Å3/Da / Density % sol: 47.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 35% PEG 400, 0.2M MgCl2, 0.1M Tris |
-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 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→45.66 Å / Num. obs: 18384 / % possible obs: 99.2 % / Redundancy: 5.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.079 / Rrim(I) all: 0.194 / Net I/σ(I): 6.2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4m3q Resolution: 2.65→45.66 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 25.763 / SU ML: 0.258 / SU R Cruickshank DPI: 0.9717 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.972 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.34 Å2 / Biso mean: 49.289 Å2 / Biso min: 14.52 Å2
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Refinement step | Cycle: final / Resolution: 2.65→45.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 7093 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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