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Yorodumi- PDB-4bky: Crystal structure of unphosphorylated Maternal Embryonic Leucine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bky | ||||||
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Title | Crystal structure of unphosphorylated Maternal Embryonic Leucine zipper Kinase (MELK) in complex with pyrrolopyrazole inhibitor | ||||||
Components | MATERNAL EMBRYONIC LEUCINE ZIPPER KINASEMELK | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase ...neural precursor cell proliferation / intrinsic apoptotic signaling pathway in response to oxidative stress / hemopoiesis / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / G2/M transition of mitotic cell cycle / cell cortex / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / apoptotic process / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Canevari, G. / Re Depaolini, S. / Cucchi, U. / Forte, B. / Carpinelli, P. / Bertrand, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural Insight Into Maternal Embryonic Leucine Zipper Kinase (Melk) Conformation and Inhibition Towards Structure- Based Drug Design. Authors: Canevari, G. / Re Depaolini, S. / Cucchi, U. / Bertrand, J.A. / Casale, E. / Perrera, C. / Forte, B. / Carpinelli, P. / Felder, E.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bky.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bky.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bky ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bky | HTTPS FTP |
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-Related structure data
Related structure data | 4bkzC 1zmuS 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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-Components
#1: Protein | Mass: 40220.539 Da / Num. of mol.: 1 / Fragment: KINASE AND UBA DOMAINS, RESIDUES 2-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase |
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#2: Chemical | ChemComp-82B / |
#3: Chemical | ChemComp-UNX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.31 % / Description: NONE |
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Crystal grow | Details: 10% PEG 3350, 0.1M BIS-TRIS PH 6.5, 0.2M SODIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→43.77 Å / Num. obs: 31014 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.83→1.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMU Resolution: 1.83→52.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 mean: 34.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→52.72 Å
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