+Open data
-Basic information
Entry | Database: PDB / ID: 3zlw | |||||||||
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Title | Crystal structure of MEK1 in complex with fragment 3 | |||||||||
Components | DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 1 MAPK/ERK KINASE 1, MEK 1, MEK1 | |||||||||
Keywords | TRANSFERASE | |||||||||
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 / labyrinthine layer development / type B pancreatic cell proliferation / 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 / labyrinthine layer development / type B pancreatic cell proliferation / MAP-kinase scaffold activity / cerebellar cortex formation / Signaling by MAP2K mutants / regulation of Golgi inheritance / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / positive regulation of axonogenesis / regulation of stress-activated MAPK cascade / Frs2-mediated activation / ERBB2-ERBB3 signaling pathway / protein kinase activator activity / endodermal cell differentiation / face development / 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 / neuron differentiation / positive regulation of protein serine/threonine kinase activity / 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 / early endosome / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / centrosome / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | |||||||||
Authors | Amaning, K. / Lowinsky, M. / Vallee, F. / Steier, V. / Marcireau, C. / Ugolini, A. / Delorme, C. / McCort, G. / Andouche, C. / Vougier, S. ...Amaning, K. / Lowinsky, M. / Vallee, F. / Steier, V. / Marcireau, C. / Ugolini, A. / Delorme, C. / McCort, G. / Andouche, C. / Vougier, S. / Llopart, S. / Halland, N. / Rak, A. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: The Use of Virtual Screening and Differential Scanning Fluorimetry for the Rapid Identification of Fragments Active Against Mek1. Authors: Amaning, K. / Lowinski, M. / Vallee, F. / Steier, V. / Marcireau, C. / Ugolini, A. / Delorme, C. / Foucalt, F. / Mccort, G. / Derimay, N. / Andouche, C. / Vougier, S. / Llopart, S. / Halland, N. / Rak, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zlw.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zlw.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zlw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/3zlw ftp://data.pdbj.org/pub/pdb/validation_reports/zl/3zlw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 38948.895 Da / Num. of mol.: 1 / Mutation: YES 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: Q02750, mitogen-activated protein kinase kinase |
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#2: Chemical | ChemComp-MT8 / ( |
#3: 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: 2.44 Å3/Da / Density % sol: 49.62 % / Description: NONE |
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Crystal grow | pH: 7.7 / Details: pH 7.7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Type: ESRF / Wavelength: 0.9336 |
Detector | Date: Apr 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9336 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→221.8 Å / Num. obs: 23238 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Biso Wilson estimate: 37.78 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.12→2.23 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→23.12 Å / Cor.coef. Fo:Fc: 0.9428 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.185 / SU Rfree Cruickshank DPI: 0.178
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Displacement parameters | Biso mean: 44.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.254 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.12→23.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.21 Å / Total num. of bins used: 12
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