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Open data
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Basic information
Entry | Database: PDB / ID: 5mah | ||||||
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Title | Crystal structure of MELK in complex with an inhibitor | ||||||
![]() | Maternal embryonic leucine zipper kinase | ||||||
![]() | TRANSFERASE / kinase / inhibitor / complex | ||||||
Function / homology | ![]() 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 / protein autophosphorylation / cell population proliferation / 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 / protein autophosphorylation / cell population proliferation / non-specific serine/threonine protein kinase / positive regulation of apoptotic process / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / calcium ion binding / apoptotic process / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Canevari, G. / Re Depaolini, S. / Casale, E. / Felder, E. / Kuster, B. / Heinzlmeir, S. | ||||||
![]() | ![]() Title: The target landscape of clinical kinase drugs. Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / ...Authors: Klaeger, S. / Heinzlmeir, S. / Wilhelm, M. / Polzer, H. / Vick, B. / Koenig, P.A. / Reinecke, M. / Ruprecht, B. / Petzoldt, S. / Meng, C. / Zecha, J. / Reiter, K. / Qiao, H. / Helm, D. / Koch, H. / Schoof, M. / Canevari, G. / Casale, E. / Depaolini, S.R. / Feuchtinger, A. / Wu, Z. / Schmidt, T. / Rueckert, L. / Becker, W. / Huenges, J. / Garz, A.K. / Gohlke, B.O. / Zolg, D.P. / Kayser, G. / Vooder, T. / Preissner, R. / Hahne, H. / Tonisson, N. / Kramer, K. / Gotze, K. / Bassermann, F. / Schlegl, J. / Ehrlich, H.C. / Aiche, S. / Walch, A. / Greif, P.A. / Schneider, S. / Felder, E.R. / Ruland, J. / Medard, G. / Jeremias, I. / Spiekermann, K. / Kuster, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83 KB | Display | ![]() |
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PDB format | ![]() | 60.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lbwC ![]() 5lbyC ![]() 5lbzC ![]() 5m5aC ![]() 5mafC ![]() 5magC ![]() 5maiC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40220.539 Da / Num. of mol.: 1 / Fragment: UNP residues 2-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q14680, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase |
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-Non-polymers , 5 types, 101 molecules ![](data/chem/img/7KD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-7KD / ~{ | ||
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#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-CL / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10-20% PEG 3350 or PEG 4000, 0.1 M BIS TRIS pH 6.5, 0.6M NaCl PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 4, 2016 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.55 Å / Num. obs: 23513 / % possible obs: 98.3 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.5 / CC1/2: 0.824 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: in house melk structure Resolution: 2→43.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.17 / 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: 38.418 Å2
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Refinement step | Cycle: 1 / Resolution: 2→43.55 Å
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Refine LS restraints |
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