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Open data
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Basic information
Entry | Database: PDB / ID: 4at3 | ||||||
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Title | CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH CPD5N | ||||||
![]() | BDNF/NT-3 GROWTH FACTORS RECEPTOR | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / brain-derived neurotrophic factor binding ...brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / brain-derived neurotrophic factor binding / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / NGF-independant TRKA activation / myelination in peripheral nervous system / Activated NTRK2 signals through PI3K / glutamate secretion / feeding behavior / neuronal action potential propagation / positive regulation of synapse assembly / positive regulation of axonogenesis / regulation of GTPase activity / central nervous system neuron development / oligodendrocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of amyloid-beta formation / negative regulation of anoikis / Activated NTRK2 signals through RAS / vasculogenesis / Activated NTRK2 signals through FRS2 and FRS3 / axon terminus / cellular response to brain-derived neurotrophic factor stimulus / learning / long-term synaptic potentiation / cellular response to amino acid stimulus / neuron migration / neuron differentiation / terminal bouton / receptor protein-tyrosine kinase / cerebral cortex development / positive regulation of neuron projection development / circadian rhythm / positive regulation of peptidyl-serine phosphorylation / early endosome membrane / protease binding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / dendritic spine / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / positive regulation of protein phosphorylation / axon / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M. | ||||||
![]() | ![]() Title: The Crystal Structures of Trka and Trkb Suggest Key Regions for Achieving Selective Inhibition. Authors: Bertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.2 KB | Display | ![]() |
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PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 757.9 KB | Display | ![]() |
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Full document | ![]() | 763.1 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aszSC ![]() 4at4C ![]() 4at5C ![]() 4f0iC 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: 34351.695 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 543-838 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16620, receptor protein-tyrosine kinase |
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#2: Chemical | ChemComp-LTI / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6 Details: THE TRKB-CPD5N COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 1.6 M AMMONIUM SULFATE, 50 MM MES, PH 6.0 AT 4 DEGREESC IN PRESENCE OF 2 MM OF INHIBITOR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 16, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→47.19 Å / Num. obs: 37068 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 23.04 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.77→1.81 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2 / % possible all: 94.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4ASZ Resolution: 1.77→24.87 Å / Cor.coef. Fo:Fc: 0.9441 / Cor.coef. Fo:Fc free: 0.9293 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.12 / SU Rfree Blow DPI: 0.112 / SU Rfree Cruickshank DPI: 0.107 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
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Displacement parameters | Biso mean: 26.78 Å2
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Refine analyze | Luzzati coordinate error obs: 0.222 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→24.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.82 Å / Total num. of bins used: 19
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