+Open data
-Basic information
Entry | Database: PDB / ID: 7b40 | ||||||
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Title | Crystal structure of c-MET bound by compound 6 | ||||||
Components | Hepatocyte growth factor receptor | ||||||
Keywords | TRANSFERASE / c-met / kinase / folded P-loop / inhibitor | ||||||
Function / homology | Function and homology information hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / MET receptor recycling ...hepatocyte growth factor receptor activity / negative regulation of guanyl-nucleotide exchange factor activity / Drug-mediated inhibition of MET activation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin receptor activity / MET receptor recycling / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / semaphorin-plexin signaling pathway / establishment of skin barrier / MET activates RAS signaling / phagocytosis / basal plasma membrane / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / InlB-mediated entry of Listeria monocytogenes into host cell / excitatory postsynaptic potential / liver development / molecular function activator activity / receptor protein-tyrosine kinase / Negative regulation of MET activity / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / cell migration / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / postsynapse / receptor complex / cell surface receptor signaling pathway / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Collie, G.W. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2021 Title: Structural Basis for Targeting the Folded P-Loop Conformation of c-MET. Authors: Collie, G.W. / Michaelides, I.N. / Embrey, K. / Stubbs, C.J. / Borjesson, U. / Dale, I.L. / Snijder, A. / Barlind, L. / Song, K. / Khurana, P. / Phillips, C. / Storer, R.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b40.cif.gz | 75.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b40.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 7b40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/7b40 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/7b40 | HTTPS FTP |
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-Related structure data
Related structure data | 7b3qC 7b3tC 7b3vC 7b3wC 7b3zC 7b41C 7b42C 7b43C 7b44C 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: 33786.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Production host: Escherichia coli (E. coli) References: UniProt: P08581, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-SWN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 % PEG4000, 10 % isopropanol, 0.1 M Na-HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→47.147 Å / Num. obs: 31621 / % possible obs: 92.9 % / Redundancy: 4.9 % / CC1/2: 0.995 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.76→1.79 Å / Num. unique obs: 1656 / CC1/2: 0.474 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: internal Resolution: 1.76→47.14 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.117
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Displacement parameters | Biso max: 110.69 Å2 / Biso mean: 36.83 Å2 / Biso min: 18.71 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.76→47.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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