+Open data
-Basic information
Entry | Database: PDB / ID: 4gk4 | ||||||
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Title | Human EphA3 Kinase domain in complex with ligand 90 | ||||||
Components | EPH receptor A3 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / RECEPTOR TYROSINE KINASE / ATP-BINDING / PHOSPHORYLATION / MEMBRANE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / negative regulation of endocytosis / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity ...fasciculation of sensory neuron axon / fasciculation of motor neuron axon / ephrin receptor activity / regulation of epithelial to mesenchymal transition / GPI-linked ephrin receptor activity / negative regulation of endocytosis / transmembrane-ephrin receptor activity / EPH-Ephrin signaling / regulation of focal adhesion assembly / regulation of GTPase activity / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / regulation of microtubule cytoskeleton organization / cellular response to retinoic acid / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / axon guidance / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cell migration / actin cytoskeleton / nuclear membrane / early endosome / cell adhesion / dendrite / extracellular region / nucleoplasm / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Dong, J. / Caflisch, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography. Authors: Lafleur, K. / Dong, J. / Huang, D. / Caflisch, A. / Nevado, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gk4.cif.gz | 76.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gk4.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gk4_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 4gk4_full_validation.pdf.gz | 753.5 KB | Display | |
Data in XML | 4gk4_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4gk4_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/4gk4 ftp://data.pdbj.org/pub/pdb/validation_reports/gk/4gk4 | HTTPS FTP |
-Related structure data
Related structure data | 4gk2C 4gk3C 2gsfS C: citing same article (ref.) S: Starting model for refinement |
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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: 40458.180 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP Residues 606-947 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EphA3 / Plasmid: p28-LIC-Thrombin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6P4R6, UniProt: P29320*PLUS, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-L90 / |
#3: 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: 1.86 Å3/Da / Density % sol: 33.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M sodium cacodylate pH 6.5, 0.15M ammonium sulf ate, 22.5% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2011 |
Radiation | Monochromator: Goebel Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→38.18 Å / Num. all: 17745 / Num. obs: 17532 / % possible obs: 98.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 21.988 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2572 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GSF Resolution: 2.1→30.777 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 22.4 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.129 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→30.777 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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