+Open data
-Basic information
Entry | Database: PDB / ID: 6jlr | ||||||
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Title | Crystal structure of wild type MNK2 in complex with inhibitor | ||||||
Components | MAP kinase-interacting serine/threonine-protein kinase 2 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Kinase / phosphorylation / inhibitor / MNK / kinase domain / TRANSFERASE / cancer / 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 / MOLECULAR REPLACEMENT / Resolution: 2.901 Å | ||||||
Authors | Baburajendran, N. / Hill, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2020 Title: Stepwise Evolution of Fragment Hits against MAPK Interacting Kinases 1 and 2. Authors: Kwiatkowski, J. / Liu, B. / Pang, S. / Ahmad, N.H.B. / Wang, G. / Poulsen, A. / Yang, H. / Poh, Y.R. / Tee, D.H.Y. / Ong, E. / Retna, P. / Dinie, N. / Kwek, P. / Wee, J.L.K. / Manoharan, V. ...Authors: Kwiatkowski, J. / Liu, B. / Pang, S. / Ahmad, N.H.B. / Wang, G. / Poulsen, A. / Yang, H. / Poh, Y.R. / Tee, D.H.Y. / Ong, E. / Retna, P. / Dinie, N. / Kwek, P. / Wee, J.L.K. / Manoharan, V. / Low, C.B. / Seah, P.G. / Pendharkar, V. / Sangthongpitag, K. / Joy, J. / Baburajendran, N. / Jansson, A.E. / Nacro, K. / Hill, J. / Keller, T.H. / Hung, A.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jlr.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jlr.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/6jlr ftp://data.pdbj.org/pub/pdb/validation_reports/jl/6jlr | HTTPS FTP |
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-Related structure data
Related structure data | 2ac3S 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: 35662.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK2, GPRK7, MNK2 / Production host: Escherichia coli (E. coli) References: UniProt: Q9HBH9, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-BV9 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: 23% polyacrylic acid 5100, 2% 2-methyl-2,4-pentane diol, 100mM Hepes pH 7.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 22, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→56.57 Å / Num. obs: 18914 / % possible obs: 78.9 % / Redundancy: 5.87 % / Biso Wilson estimate: 86.73 Å2 / Rmerge(I) obs: 0.23 / Rrim(I) all: 0.251 / Χ2: 1.15 / Net I/σ(I): 4.6 / Num. measured all: 111944 / Scaling rejects: 840 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AC3 Resolution: 2.901→28.283 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.17 Å2 / Biso mean: 86.4006 Å2 / Biso min: 35.41 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.901→28.283 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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