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Yorodumi- PDB-5mjb: Kinase domain of human EphB1, G703C mutant, covalently bound to a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mjb | ||||||
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Title | Kinase domain of human EphB1, G703C mutant, covalently bound to a quinazoline-based inhibitor | ||||||
Components | Ephrin type-B receptor 1 | ||||||
Keywords | TRANSFERASE / Receptor tyrosine kinase / kinase domain / Inhibitor / covalent | ||||||
Function / homology | Function and homology information skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development ...skeletal muscle satellite cell activation / negative regulation of satellite cell differentiation / hindbrain tangential cell migration / negative regulation of skeletal muscle satellite cell proliferation / optic nerve morphogenesis / axon guidance receptor activity / central nervous system projection neuron axonogenesis / immunological synapse formation / filopodium tip / dendritic spine development / camera-type eye morphogenesis / transmembrane-ephrin receptor activity / dendritic spine morphogenesis / neural precursor cell proliferation / positive regulation of synapse assembly / EPH-Ephrin signaling / Ephrin signaling / retinal ganglion cell axon guidance / establishment of cell polarity / cell-substrate adhesion / detection of temperature stimulus involved in sensory perception of pain / regulation of JNK cascade / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / EPHB-mediated forward signaling / neurogenesis / regulation of ERK1 and ERK2 cascade / cell chemotaxis / axon guidance / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / early endosome membrane / angiogenesis / protein autophosphorylation / membrane raft / axon / glutamatergic synapse / dendrite / protein-containing complex binding / endoplasmic reticulum / 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: 2.23 Å | ||||||
Authors | Kung, A. / Schimpl, M. / Chen, Y.-C. / Overman, R.C. / Zhang, C. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: A Chemical-Genetic Approach to Generate Selective Covalent Inhibitors of Protein Kinases. Authors: Kung, A. / Schimpl, M. / Ekanayake, A. / Chen, Y.C. / Overman, R. / Zhang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mjb.cif.gz | 244.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mjb.ent.gz | 196.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mjb_validation.pdf.gz | 728.9 KB | Display | wwPDB validaton report |
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Full document | 5mjb_full_validation.pdf.gz | 732.6 KB | Display | |
Data in XML | 5mjb_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 5mjb_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/5mjb ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mjb | HTTPS FTP |
-Related structure data
Related structure data | 5mjaC 3zfxS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 34903.703 Da / Num. of mol.: 2 / Mutation: G703C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPHB1, ELK, EPHT2, HEK6, NET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD References: UniProt: P54762, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.08 % / Description: hexagonal plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 18 % PEG3350, 0.1-0.2 M ammonium sulfate and 0.1 M PCTP (Sodium propionate, Sodium cacodylate trihydrate, Bis-Tris propane) buffer pH 6-9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→58.84 Å / Num. obs: 47109 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 51.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.707 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.622 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZFX Resolution: 2.23→58.84 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.152
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Displacement parameters | Biso mean: 59.29 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.23→58.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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