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Yorodumi- PDB-4d3c: Crystal structure of the NK1 domain of HGF in complex with anti-H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d3c | ||||||
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Title | Crystal structure of the NK1 domain of HGF in complex with anti-HGF monoclonal antibody SFN68. | ||||||
Components |
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Keywords | PROTEIN BINDING | ||||||
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 / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / 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 / negative regulation of peptidyl-serine phosphorylation / Interleukin-7 signaling / cell chemotaxis / negative regulation of autophagy / liver development / platelet alpha granule lumen / epithelial cell proliferation / growth factor activity / cell morphogenesis / Negative regulation of MET activity / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of peptidyl-tyrosine phosphorylation / Platelet degranulation / PIP3 activates AKT signaling / 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 / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) ORYCTOLAGUS CUNICULUS (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Kang, Y.J. / Kim, K.L. / Cho, H.S. / Chung, J.H. | ||||||
Citation | Journal: to be published Title: A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist. Authors: Kang, Y.J. / Kim, K.L. / Cho, H.S. / Chung, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d3c.cif.gz | 121.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d3c.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 4d3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3c ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3c | 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
#1: Protein | Mass: 22242.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-210 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P14210 |
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#2: Antibody | Mass: 23230.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT/HUMAN CHIMERIC ANTIBODY / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) |
#3: Antibody | Mass: 22974.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT/HUMAN CHIMERIC ANTIBODY / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: U3KM01*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Type: PAL/PLS / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→29.79 Å / Num. obs: 25541 / % possible obs: 95.5 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1JPT, 1NK1. Resolution: 2.62→29.79 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.56 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.511 / ESU R Free: 0.328 / 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: 85.704 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→29.79 Å
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