+Open data
-Basic information
Entry | Database: PDB / ID: 6ck3 | ||||||
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Title | Co-crytsal Structure of MNK2 in Complex With an Inhibitor | ||||||
Components | MAP kinase-interacting serine/threonine-protein kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE Inhibitor / mnk2 inhibitor / TRANSFERASE-TRANSFERASE Inhibitor complex | ||||||
Function / homology | Function and homology information calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding ...calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Han, Q. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structure-based Design of Pyridone-Aminal eFT508 Targeting Dysregulated Translation by Selective Mitogen-activated Protein Kinase Interacting Kinases 1 and 2 (MNK1/2) Inhibition. Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. ...Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. / Jessen, K.A. / Molter, J. / Murphy, D. / Neal, M. / Parker, G.S. / Shaghafi, M. / Sperry, S. / Staunton, J. / Stumpf, C.R. / Thompson, P.A. / Tran, C. / Webber, S.E. / Wegerski, C.J. / Zheng, H. / Webster, K.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ck3.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ck3.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ck3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/6ck3 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/6ck3 | HTTPS FTP |
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-Related structure data
Related structure data | 6cj5C 6cjeC 6cjhC 6cjwC 6cjyC 6ck6C 6ckiC 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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Unit cell |
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-Components
#1: Protein | Mass: 35604.461 Da / Num. of mol.: 1 / Mutation: D228G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK2, GPRK7, MNK2 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 References: UniProt: Q9HBH9, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-F67 / ( |
#4: Chemical | ChemComp-CL / |
#5: 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: 3.22 Å3/Da / Density % sol: 61.79 % |
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Crystal grow | Temperature: 300.11 K / Method: vapor diffusion, sitting drop Details: 20-30% (w/v) polyacrylic acid 5100, 1-5% PEG 400, and 50 mM Hepes (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→56.7 Å / Num. obs: 11166 / % possible obs: 98 % / Redundancy: 4 % / Net I/σ(I): 4 |
Reflection shell | Resolution: 2.9→2.975 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.21 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 106.718 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→40 Å
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Refine LS restraints |
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