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Yorodumi- PDB-3eqd: X-ray structure of the human mitogen-activated protein kinase kin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eqd | ||||||
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Title | X-ray structure of the human mitogen-activated protein kinase kinase 1 (MEK1) in a binary complex with ATP-GS and MG2P | ||||||
Components | Dual specificity mitogen-activated protein kinase kinase 1 | ||||||
Keywords | TRANSFERASE / MEK1 KINASE / ATP-binding / Disease mutation / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Tyrosine-protein kinase | ||||||
Function / homology | Function and homology information epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants ...epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / placenta blood vessel development / regulation of axon regeneration / mitogen-activated protein kinase kinase / type B pancreatic cell proliferation / labyrinthine layer development / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants / regulation of Golgi inheritance / trachea formation / regulation of early endosome to late endosome transport / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / positive regulation of axonogenesis / Frs2-mediated activation / protein kinase activator activity / ERBB2-ERBB3 signaling pathway / face development / endodermal cell differentiation / MAPK3 (ERK1) activation / Bergmann glial cell differentiation / MAP kinase kinase activity / thyroid gland development / Uptake and function of anthrax toxins / Schwann cell development / keratinocyte differentiation / ERK1 and ERK2 cascade / myelination / protein serine/threonine/tyrosine kinase activity / protein serine/threonine kinase activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / insulin-like growth factor receptor signaling pathway / thymus development / Signal transduction by L1 / cell motility / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein serine/threonine kinase activity / neuron differentiation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome / heart development / scaffold protein binding / protein tyrosine kinase activity / positive regulation of ERK1 and ERK2 cascade / early endosome / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / focal adhesion / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / endoplasmic reticulum / signal transduction / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Fischmann, T.O. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors. Authors: Fischmann, T.O. / Smith, C.K. / Mayhood, T.W. / Myers, J.E. / Reichert, P. / Mannarino, A. / Carr, D. / Zhu, H. / Wong, J. / Yang, R.S. / Le, H.V. / Madison, V.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eqd.cif.gz | 82.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eqd.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 3eqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eqd ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eqd | HTTPS FTP |
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-Related 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 40113.215 Da / Num. of mol.: 1 / Fragment: Protein kinase domain, UNP residues 35-393 / Mutation: S265N, S266K, Y267F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 References: UniProt: Q02750, mitogen-activated protein kinase kinase |
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-Non-polymers , 5 types, 136 molecules
#2: Chemical | ChemComp-AGS / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CA / |
#5: Chemical | ChemComp-NA / |
#6: 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: 2.37 Å3/Da / Density % sol: 48.16 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M TRIS-CL, pH 8.0; 18% PEG 4000; 0.2M CALCIUM CHLORIDE; 3% DMSO, VAPOR DIFFUSION HANGING DROP, temperature 281K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→30 Å / Num. obs: 23271 / % possible obs: 97.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.015 / Net I/σ(I): 10.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.1→25 Å / σ(F): 0 / σ(I): -3
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Displacement parameters | Biso mean: 52.292 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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