+Open data
-Basic information
Entry | Database: PDB / ID: 5lsp | ||||||
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Title | 107_A07 Fab in complex with fragment of the Met receptor | ||||||
Components |
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Keywords | TRANSFERASE / Fab / beta propeller / Ig-like domain / cell signalling / Met receptor / antibody binding | ||||||
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 / positive regulation of endothelial cell chemotaxis ...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 / positive regulation of endothelial cell chemotaxis / 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 / 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 / MECP2 regulates neuronal receptors and channels / positive regulation of microtubule polymerization / negative regulation of autophagy / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / liver development / molecular function activator activity / Negative regulation of MET activity / receptor protein-tyrosine kinase / neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / 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 phosphatase binding / protein tyrosine kinase activity / cell surface receptor signaling pathway / receptor complex / phosphorylation / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular region / ATP binding / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.605 Å | ||||||
Authors | DiCara, D. / Chirgadze, D.Y. / Pope, A. / Karatt-Vellatt, A. / Winter, A. / van den Heuvel, J. / Gherardi, E. / McCafferty, J. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Characterization and structural determination of a new anti-MET function-blocking antibody with binding epitope distinct from the ligand binding domain. Authors: DiCara, D.M. / Chirgadze, D.Y. / Pope, A.R. / Karatt-Vellatt, A. / Winter, A. / Slavny, P. / van den Heuvel, J. / Parthiban, K. / Holland, J. / Packman, L.C. / Mavria, G. / Hoffmann, J. / ...Authors: DiCara, D.M. / Chirgadze, D.Y. / Pope, A.R. / Karatt-Vellatt, A. / Winter, A. / Slavny, P. / van den Heuvel, J. / Parthiban, K. / Holland, J. / Packman, L.C. / Mavria, G. / Hoffmann, J. / Birchmeier, W. / Gherardi, E. / McCafferty, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lsp.cif.gz | 258.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lsp.ent.gz | 209 KB | Display | PDB format |
PDBx/mmJSON format | 5lsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/5lsp ftp://data.pdbj.org/pub/pdb/validation_reports/ls/5lsp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Hepatocyte growth factor ... , 2 types, 4 molecules APXY
#1: Protein | Mass: 25592.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pA71d / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P08581, receptor protein-tyrosine kinase #4: Protein/peptide | Mass: 1627.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MET / Plasmid: pA71d / Cell line (production host): Lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P08581, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 4 molecules HSLT
#2: Antibody | Mass: 23891.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 23504.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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-Sugars / Non-polymers , 2 types, 90 molecules
#5: Sugar | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 20,000, 20% PEG 550-MME, 0.1M Trizma/Bicine pH 8.5, 0.03M magnesium chloride, 0.03M calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.91376 Å | ||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 29, 2012 | ||||||||||||||||||
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.91376 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.6→48.95 Å / Num. obs: 49099 / % possible obs: 99 % / Redundancy: 5.5 % / Biso Wilson estimate: 50.2 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11.7 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.605→48.942 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 27.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.605→48.942 Å
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Refine LS restraints |
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LS refinement shell |
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