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- PDB-4crp: Solution structure of a TrkAIg2 domain construct for use in drug ... -

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Basic information

Entry
Database: PDB / ID: 4crp
TitleSolution structure of a TrkAIg2 domain construct for use in drug discovery
ComponentsHIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
KeywordsTRANSFERASE / TRKAIG2 / NMR CONSTRUCT / PAIN / ALZHEIMERS
Function / homology
Function and homology information


neurotrophin p75 receptor binding / behavioral response to formalin induced pain / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / neurotrophin receptor activity / mechanoreceptor differentiation ...neurotrophin p75 receptor binding / behavioral response to formalin induced pain / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / Signalling to STAT3 / programmed cell death involved in cell development / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / axonogenesis involved in innervation / nerve growth factor signaling pathway / nerve growth factor binding / Sertoli cell development / Retrograde neurotrophin signalling / sympathetic nervous system development / NGF-independant TRKA activation / Signalling to p38 via RIT and RIN / ARMS-mediated activation / positive regulation of programmed cell death / positive regulation of Ras protein signal transduction / positive regulation of synapse assembly / PI3K/AKT activation / Frs2-mediated activation / neurotrophin TRK receptor signaling pathway / detection of temperature stimulus involved in sensory perception of pain / response to electrical stimulus / GPI-linked ephrin receptor activity / peptidyl-tyrosine autophosphorylation / Signalling to RAS / detection of mechanical stimulus involved in sensory perception of pain / neuron development / response to axon injury / positive regulation of GTPase activity / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / B cell differentiation / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / response to nutrient levels / peptidyl-tyrosine phosphorylation / cellular response to nerve growth factor stimulus / positive regulation of NF-kappaB transcription factor activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / cellular response to nicotine / kinase binding / circadian rhythm / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / late endosome membrane / late endosome / protein autophosphorylation / protein tyrosine kinase activity / early endosome membrane / spermatogenesis / neuron apoptotic process / negative regulation of neuron apoptotic process / learning or memory / early endosome / endosome membrane / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphorylation / response to xenobiotic stimulus / axon / negative regulation of cell population proliferation / neuronal cell body / dendrite / negative regulation of apoptotic process / cell surface / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...High affinity nerve growth factor receptor NTRK1 / Tyrosine kinase receptor A, transmembrane domain / Tyrosine kinase receptor A trans-membrane domain / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Leucine rich repeat / : / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA 2.3
AuthorsShoemark, D.K. / Fahey, M. / Williams, C. / Sessions, R.B. / Crump, M.P. / Allen-Birt, S.J.
CitationJournal: 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
DepositionFeb 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Apr 27, 2016Group: Atomic model / Derived calculations / Other
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)11,7921
Polymers11,7921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 250LOWEST ENERGY, LEAST VIOLATION
RepresentativeModel #1

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Components

#1: Protein HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR / NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1 / TRK1-TRANSFORMING TYROSINE KINASE PROTEIN / ...NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 1 / TRK1-TRANSFORMING TYROSINE KINASE PROTEIN / TROPOMYOSIN-RELATED KINASE A / TYROSINE KINASE RECEPTOR / TYROSINE KINASE RECEPTOR A / TRK-A / GP140TRK / P140-TRKA


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
Has protein modificationY
Sequence detailsENGINEERED N-TERMINAL ASP TAG (RESIDUES 1-5) AND DISULPHIDE BOND.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131HNCA
141HN(CA)CB
151C(CO)NH
161(H)CCH-TOCSY
171H(CCO)NH
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 13C, 15N-LABELED SAMPLES

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Sample preparation

DetailsContents: 90% H2O, 10% D2O
Sample conditionsIonic strength: 10 mM / pH: 6.9 / Pressure: 1.0 atm / Temperature: 293.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON, WARRENrefinement
CNS1.2structure solution
RefinementMethod: ARIA 2.3 / Software ordinal: 1 / Details: WATER REFINED USING THE RECOORD PROTOCOL
NMR ensembleConformer selection criteria: LOWEST ENERGY, LEAST VIOLATION
Conformers calculated total number: 250 / Conformers submitted total number: 25

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