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- PDB-5mo9: Structure of human TrkB receptor ligand binding domain in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mo9 | ||||||
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Title | Structure of human TrkB receptor ligand binding domain in complex with the Fab frgment of antibody AB20 | ||||||
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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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoerer, S. | ||||||
![]() | ![]() Title: Pharmaceutical Characterization of Tropomyosin Receptor Kinase B-Agonistic Antibodies on Human Induced Pluripotent Stem (hiPS) Cell-Derived Neurons. Authors: Traub, S. / Stahl, H. / Rosenbrock, H. / Simon, E. / Florin, L. / Hospach, L. / Horer, S. / Heilker, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.9 KB | Display | ![]() |
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PDB format | ![]() | 113.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1hcfS S: Starting model for refinement |
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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: Antibody | Mass: 23675.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23931.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 16909.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment: Ligand binding domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q16620, ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 44.47 % / Description: rod-shaped |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 6% w/v PEG 3350, 25 mM Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2014 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.594→37.402 Å / Num. obs: 18392 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 34.87 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.158 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.594→2.639 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.963 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.744 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1hcf Resolution: 2.594→37 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.466 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.513 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.253
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Displacement parameters | Biso mean: 47.98 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.594→37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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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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