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- PDB-3sp8: Crystal structure of NK2 in complex with fractionated Heparin DP10 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sp8 | ||||||
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Title | Crystal structure of NK2 in complex with fractionated Heparin DP10 | ||||||
![]() | Hepatocyte growth factor alpha chain | ||||||
![]() | HORMONE / kringle domain / MET Tyrosine Kinase | ||||||
Function / homology | ![]() 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 / Interleukin-7 signaling / negative regulation of autophagy / cell chemotaxis / platelet alpha granule lumen / liver development / 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 / 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 / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Recacha, R. / Mulloy, B. / Gherardi, E. | ||||||
![]() | ![]() Title: Crystal structure of NK2 in complex with fractionated Heparin DP10 Authors: Recacha, R. / Mulloy, B. / Gherardi, E. #1: ![]() Title: Crystal structures of NK1 heparin complexes reveal the basis for NK1 activity and enable engineering of potent agonists of the MET receptor Authors: Lietha, D. / Chirgadze, D.Y. / L Blundell, T. / Gherardi, E. / Mulloy, B. #2: ![]() Title: Structural basis for agonism and antagonism of hepatocyte growth factor Authors: Tolbert, W.D. / Daugherty-Holtrop, J. / Vande Woude, G. / Xu, H.E. / Gherardi, E. #3: ![]() Title: Heparin-induced cis- and trans-Dimerization Modes of the Thrombospondin-1 N-terminal Domain Authors: Tan, K. / Duquette, M. / Liu, J.H. / Shanmugasundaram, K. / Joachimiak, A. / Gallagher, J.T. / Rigby, A.C. / Wang, J.H. / Lawler, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 244 KB | Display | ![]() |
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PDB format | ![]() | 196.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 490.4 KB | Display | ![]() |
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Full document | ![]() | 498.6 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nh4S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30910.119 Da / Num. of mol.: 2 / Fragment: NK2 / Mutation: G146D, C214S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 5 types, 378 molecules ![](data/chem/img/MRD.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MRD / ( #3: Chemical | ChemComp-MES / #4: Chemical | ChemComp-MPD / ( | #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.29 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM MES pH=6.0, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 21K, temperature 294K |
-Data collection
Diffraction | Mean temperature: 172 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2011 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→65.8 Å / Num. all: 107330 / Num. obs: 54379 / % possible obs: 99.76 % / Observed criterion σ(F): 1.38 |
Reflection shell | Highest resolution: 1.86 Å / % possible all: 99.76 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NH4 Resolution: 1.86→65.8 Å / SU ML: 0.57 / Cross valid method: Maximum Likelyhood / σ(F): 1.38 / Phase error: 22.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.503 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.86→65.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -29.1929 Å / Origin y: 26.8444 Å / Origin z: -16.1371 Å
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Refinement TLS group | Selection details: all |