+Open data
-Basic information
Entry | Database: PDB / ID: 6fnl | ||||||
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Title | Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase | ||||||
Components | Ephrin type-B receptor 4 | ||||||
Keywords | TRANSFERASE / Protein Tyrosine Kinase | ||||||
Function / homology | Function and homology information 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 / receptor protein-tyrosine kinase ...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 / receptor protein-tyrosine kinase / angiogenesis / protein autophosphorylation / receptor complex / cell adhesion / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 Å | ||||||
Authors | Kudlinzki, D. / Troester, A. / Witt, K. / Linhard, V.L. / Saxena, K. / Schwalbe, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: ChemMedChem / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fnl.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fnl.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/6fnl ftp://data.pdbj.org/pub/pdb/validation_reports/fn/6fnl | HTTPS FTP |
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-Related structure data
Related structure data | 6fnfC 6fngC 6fnhC 6fniC 6fnjC 6fnkC 6fnmC 2vwuS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 33488.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB4, HTK, MYK1, TYRO11 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P54760, receptor protein-tyrosine kinase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % PEG5000 MME, 15 % Glycerol, 0.1 M TRIS pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.269→43.112 Å / Num. obs: 74570 / % possible obs: 97.8 % / Redundancy: 6.69 % / Biso Wilson estimate: 28.32 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.269→1.34 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.23 / Num. unique obs: 11399 / CC1/2: 0.126 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VWU Resolution: 1.269→43.112 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.269→43.112 Å
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Refine LS restraints |
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LS refinement shell |
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