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Yorodumi- PDB-3mkp: Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mkp | |||||||||
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Title | Crystal structure of 1K1 mutant of Hepatocyte Growth Factor/Scatter Factor fragment NK1 in complex with heparin | |||||||||
Components | Hepatocyte growth factor | |||||||||
Keywords | HORMONE / growth factor / supramolecular assembly / HGF/SF / Met receptor / NK1 | |||||||||
Function / homology | Function and homology information regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / epithelial cell proliferation / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / platelet alpha granule lumen / liver development / negative regulation of inflammatory response / growth factor activity / cell morphogenesis / Negative regulation of MET activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / Platelet degranulation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Gherardi, E. / Chirgadze, D.Y. / Blundell, T.L. | |||||||||
Citation | Journal: To be Published Title: Engineering a fragment of Hepatocyte Growth Factor/Scatter Factor for tissue and organ regeneration Authors: Gherardi, E. / Chirgadze, D.Y. / Bocci, M. / Brocchieri, C. / Bevan, D. / Kajstura, J. / Esposito, G. / Lietha, D. / Rota, M. / Leri, A. / Mallorqui-Fernandez, N. / Bandyopadhyay, A. / ...Authors: Gherardi, E. / Chirgadze, D.Y. / Bocci, M. / Brocchieri, C. / Bevan, D. / Kajstura, J. / Esposito, G. / Lietha, D. / Rota, M. / Leri, A. / Mallorqui-Fernandez, N. / Bandyopadhyay, A. / Youles, M. / Mulloy, B. / Rowe, A. / Alison, M. / Edwards, D. / Vannini, V. / Blundell, T. / Anversa, P. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Coupling growth-factor engineering with nanotechnology for therapeutic angiogenesis Authors: Roy, R.S. / Soni, S. / Harfouche, R. / Vasudevan, P.R. / Holmes, O. / de Jonge, H. / Rowe, A. / Paraskar, A. / Hentschel, D.M. / Chirgadze, D. / Blundell, T.L. / Gherardi, E. / Mashelkar, R.A. / Sengupta, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mkp.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mkp.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mkp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3mkp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3mkp_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 3mkp_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/3mkp ftp://data.pdbj.org/pub/pdb/validation_reports/mk/3mkp | HTTPS FTP |
-Related structure data
Related structure data | 1bhtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 21116.074 Da / Num. of mol.: 4 / Fragment: UNP residues 28-210 / Mutation: K132E, R134E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9K / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P14210 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-SGN / |
-Non-polymers , 3 types, 109 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-EPE / #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: 2.94 Å3/Da / Density % sol: 58.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.243M Ammonium Sulfate, 22.295% PEG 3350, 0.1M Na-Hepes pH 7.5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 25301 / Num. obs: 25225 / % possible obs: 99.7 % / Observed criterion σ(I): 2.5 / Redundancy: 7.9 % / Biso Wilson estimate: 61.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.498 / Num. unique all: 1661 / Rsym value: 0.498 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BHT Resolution: 2.81→49.69 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.862 / SU B: 26.614 / SU ML: 0.267 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.489 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.405 Å2
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Refinement step | Cycle: LAST / Resolution: 2.81→49.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.807→2.88 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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