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Yorodumi- PDB-4crp: Solution structure of a TrkAIg2 domain construct for use in drug ... -
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-Basic information
Entry | Database: PDB / ID: 4crp | ||||||
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Title | Solution structure of a TrkAIg2 domain construct for use in drug discovery | ||||||
Components | HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR | ||||||
Keywords | TRANSFERASE / TRKAIG2 / NMR CONSTRUCT / PAIN / ALZHEIMERS | ||||||
Function / homology | Function and homology information behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation ...behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / Retrograde neurotrophin signalling / nerve growth factor binding / NGF-independant TRKA activation / sympathetic nervous system development / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / response to axon injury / neuron development / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / axon guidance / receptor protein-tyrosine kinase / kinase binding / positive regulation of neuron projection development / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / learning or memory / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / endosome membrane / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein phosphorylation / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / ARIA 2.3 | ||||||
Authors | Shoemark, D.K. / Fahey, M. / Williams, C. / Sessions, R.B. / Crump, M.P. / Allen-Birt, S.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Design and Nuclear Magnetic Resonance (NMR) Structure Determination of the Second Extracellular Immunoglobulin Tyrosine Kinase a (Trkaig2) Domain Construct for Binding Site Elucidation in Drug Discovery Authors: Allen, S.J. / Watson, J.J. / Shoemark, D.K. / Barua, N.U. / Patel, N.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4crp.cif.gz | 843.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crp.ent.gz | 723.5 KB | Display | PDB format |
PDBx/mmJSON format | 4crp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4crp_validation.pdf.gz | 472.3 KB | Display | wwPDB validaton report |
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Full document | 4crp_full_validation.pdf.gz | 817.4 KB | Display | |
Data in XML | 4crp_validation.xml.gz | 93.7 KB | Display | |
Data in CIF | 4crp_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crp ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crp | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11792.068 Da / Num. of mol.: 1 Fragment: EXTRACELLULAR NGF BINDING DOMAIN, RESIDUES 270-383 Mutation: YES Source method: isolated from a genetically manipulated source Details: P285C, F367C INTRODUCED TO ADD A DISULPHIDE BOND TO IMPROVE PROTEIN STABILITY Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P04629, receptor protein-tyrosine kinase |
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Sequence details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 13C, 15N-LABELED SAMPLES |
-Sample preparation
Details | Contents: 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 10 mM / pH: 6.9 / Pressure: 1.0 atm / Temperature: 293.0 K |
-NMR measurement
NMR spectrometer | Type: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: ARIA 2.3 / Software ordinal: 1 / Details: WATER REFINED USING THE RECOORD PROTOCOL | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY, LEAST VIOLATION Conformers calculated total number: 250 / Conformers submitted total number: 25 |