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- PDB-6fni: Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fni | ||||||
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Title | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with NVP-BHG712 | ||||||
![]() | Ephrin type-B receptor 4 | ||||||
![]() | TRANSFERASE / Inhibitor / Complex / Protein Tyrosine Kinase | ||||||
Function / homology | ![]() ephrin receptor activity / transmembrane-ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity ...ephrin receptor activity / transmembrane-ephrin receptor activity / cell migration involved in sprouting angiogenesis / EPH-Ephrin signaling / Ephrin signaling / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / heart morphogenesis / EPHB-mediated forward signaling / transmembrane receptor protein tyrosine kinase activity / axon guidance / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / dendrite / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Saxena, K. / Schwalbe, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. Authors: Troster, A. / Heinzlmeir, S. / Berger, B.T. / Gande, S.L. / Saxena, K. / Sreeramulu, S. / Linhard, V. / Nasiri, A.H. / Bolte, M. / Muller, S. / Kuster, B. / Medard, G. / Kudlinzki, D. / Schwalbe, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 750.5 KB | Display | ![]() |
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Full document | ![]() | 756 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fnfC ![]() 6fngC ![]() 6fnhC ![]() 6fnjC ![]() 6fnkC ![]() 6fnlC ![]() 6fnmC ![]() 2vwuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33488.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P54760, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-DXH / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 % PEG5000 MME, 0.15 M MgCl2, 15 % Glycerol, 0.1 M TRIS pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708479 Å / Relative weight: 1 |
Reflection | Resolution: 1.468→49.46 Å / Num. obs: 67505 / % possible obs: 99.8 % / Redundancy: 20 % / Biso Wilson estimate: 32.43 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.134 / Net I/σ(I): 13.28 |
Reflection shell | Resolution: 1.468→1.56 Å / Redundancy: 19.6 % / Mean I/σ(I) obs: 0.34 / Num. unique obs: 10762 / CC1/2: 0.112 / % possible all: 98.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 2VWU Resolution: 1.468→49.457 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.468→49.457 Å
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Refine LS restraints |
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LS refinement shell |
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