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- PDB-4at5: CRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580 -

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Entry
Database: PDB / ID: 4at5
TitleCRYSTAL STRUCTURE OF TRKB KINASE DOMAIN IN COMPLEX WITH GW2580
ComponentsBDNF/NT-3 GROWTH FACTORS RECEPTOR
KeywordsTRANSFERASE
Function / homology
Function and homology information


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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / peripheral nervous system neuron development / brain-derived neurotrophic factor binding / mechanoreceptor differentiation ...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 / trans-synaptic signaling by BDNF, modulating synaptic transmission / peripheral nervous system neuron development / brain-derived neurotrophic factor binding / 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 / feeding behavior / positive regulation of axonogenesis / neuronal action potential propagation / positive regulation of synapse assembly / glutamate secretion / regulation of GTPase activity / negative regulation of amyloid-beta formation / central nervous system neuron development / oligodendrocyte differentiation / negative regulation of anoikis / Activated NTRK2 signals through RAS / Activated NTRK2 signals through FRS2 and FRS3 / vasculogenesis / cellular response to brain-derived neurotrophic factor stimulus / axon terminus / cell surface receptor protein tyrosine kinase signaling pathway / learning / cellular response to amino acid stimulus / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / terminal bouton / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / cerebral cortex development / positive regulation of neuron projection development / long-term synaptic potentiation / circadian rhythm / neuron differentiation / neuron migration / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / protein autophosphorylation / early endosome membrane / dendritic spine / negative regulation of neuron apoptotic process / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / postsynaptic density / axon / positive regulation of cell population proliferation / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
BDNF/NT-3 growth factors receptor NTRK2 / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site ...BDNF/NT-3 growth factors receptor NTRK2 / Growth factor receptor NTRK / Growth factor receptor NTRK, leucine rich repeat C-terminal / Leucine rich repeat C-terminal motif / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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. / Immunoglobulin I-set / Immunoglobulin I-set domain / Leucine rich repeat / : / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MUJ / BDNF/NT-3 growth factors receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBertrand, T. / Kothe, M. / Liu, J. / Dupuy, A. / Rak, A. / Berne, P.F. / Davis, S. / Gladysheva, T. / Valtre, C. / Crenne, J.Y. / Mathieu, M.
CitationJournal: J.Mol.Biol. / Year: 2012
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
DepositionMay 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jul 24, 2013Group: Refinement description
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: BDNF/NT-3 GROWTH FACTORS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8103
Polymers34,3521
Non-polymers4592
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.540, 94.190, 46.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein BDNF/NT-3 GROWTH FACTORS RECEPTOR / GP145-TRKB / TRK-B / NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 2 / TRKB TYROSINE KINASE / ...GP145-TRKB / TRK-B / NEUROTROPHIC TYROSINE KINASE RECEPTOR TYPE 2 / TRKB TYROSINE KINASE / TROPOMYOSIN-RELATED KINASE B


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.) HOMO SAPIENS (human) / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q16620, receptor protein-tyrosine kinase
#2: Chemical ChemComp-MUJ / 5-{3-methoxy-4-[(4-methoxybenzyl)oxy]benzyl}pyrimidine-2,4-diamine


Mass: 366.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N4O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8
Details: THE TRKB-GW2580 COMPLEX WAS OBTAINED BY COCRYSTALLIZATION IN 2.4 M NA-FORMATE, 50 MM HEPES, PH 8.0 AT 4 DEGREES C IN PRESENCE OF 2 MM OF INHIBITOR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97626
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2011 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.71→47.09 Å / Num. obs: 40698 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 16.09 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6
Reflection shellResolution: 1.71→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.7 / % possible all: 79

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ASZ

4asz


Resolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9399 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.085
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 4025 9.89 %RANDOM
Rwork0.1582 ---
obs-40682 95.35 %-
Displacement parametersBiso mean: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1--3.496 Å20 Å20 Å2
2--1.9515 Å20 Å2
3---1.5444 Å2
Refine analyzeLuzzati coordinate error obs: 0.154 Å
Refinement stepCycle: LAST / Resolution: 1.71→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 33 365 2768
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012460HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953325HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d862SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes376HARMONIC5
X-RAY DIFFRACTIONt_it2460HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion14.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion303SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3282SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1884 204 9.97 %
Rwork0.1689 1842 -
all0.171 2046 -
obs--95.35 %

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