+Open data
-Basic information
Entry | Database: PDB / ID: 7b3z | ||||||
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Title | Crystal structure of c-MET bound by compound 5 | ||||||
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 / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / endothelial cell morphogenesis / 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 / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / endothelial cell morphogenesis / semaphorin receptor activity / MET receptor recycling / 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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / liver development / basal plasma membrane / excitatory postsynaptic potential / InlB-mediated entry of Listeria monocytogenes into host cell / molecular function activator activity / receptor protein-tyrosine kinase / neuron differentiation / Negative regulation of MET activity / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / 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: 1.8 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 | 7b3z.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b3z.ent.gz | 52.9 KB | Display | PDB format |
PDBx/mmJSON format | 7b3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b3z_validation.pdf.gz | 746.5 KB | Display | wwPDB validaton report |
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Full document | 7b3z_full_validation.pdf.gz | 747.9 KB | Display | |
Data in XML | 7b3z_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 7b3z_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/7b3z ftp://data.pdbj.org/pub/pdb/validation_reports/b3/7b3z | HTTPS FTP |
-Related structure data
Related structure data | 7b3qC 7b3tC 7b3vC 7b3wC 7b40C 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-DMS / |
#3: Chemical | ChemComp-SV8 / |
#4: 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: 2.54 Å3/Da / Density % sol: 51.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG10000, 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: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→21.34 Å / Num. obs: 31317 / % possible obs: 98.7 % / Redundancy: 3 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Num. unique obs: 1480 / CC1/2: 0.548 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: internal Resolution: 1.8→21.34 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso max: 93.08 Å2 / Biso mean: 37.64 Å2 / Biso min: 18.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→21.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
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