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- PDB-6pl1: TRK-A IN COMPLEX WITH LIGAND 1B -

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Basic information

Entry
Database: PDB / ID: 6pl1
TitleTRK-A IN COMPLEX WITH LIGAND 1B
ComponentsHigh affinity nerve growth factor receptor
KeywordsTRANSFERASE / TRK-A KINASE DOMAIN HIGH AFFINITY NERVE GROWTH FACTOR RECEPTOR
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 / neurotrophin receptor activity / programmed cell death involved in cell development / 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 / neurotrophin receptor activity / programmed cell death involved in cell development / mechanoreceptor differentiation / nerve growth factor receptor activity / neurotrophin binding / nerve growth factor signaling pathway / axonogenesis involved in innervation / Sertoli cell development / Retrograde neurotrophin signalling / nerve growth factor binding / sympathetic nervous system development / NGF-independant TRKA activation / 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 / neurotrophin TRK receptor signaling pathway / detection of temperature stimulus involved in sensory perception of pain / Signalling to RAS / response to axon injury / neuron development / 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 GTPase activity / B cell differentiation / positive regulation of synaptic transmission, glutamatergic / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to nerve growth factor stimulus / response to nutrient levels / 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 / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / cellular response to nicotine / kinase binding / recycling endosome membrane / circadian rhythm / positive regulation of angiogenesis / neuron projection development / positive regulation of NF-kappaB transcription factor activity / late endosome membrane / late endosome / protein autophosphorylation / protein tyrosine kinase activity / early endosome membrane / neuron apoptotic process / spermatogenesis / negative regulation of neuron apoptotic process / learning or memory / early endosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of ERK1 and ERK2 cascade / endosome membrane / 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 / 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-OOJ / High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSubramanian, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2019
Title: Lead identification and characterization of hTrkA type 2 inhibitors.
Authors: Subramanian, G. / Zhu, Y. / Bowen, S.J. / Roush, N. / White, J.A. / Huczek, D. / Zachary, T. / Javens, C. / Williams, T. / Janssen, A. / Gonzales, A.
History
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: High affinity nerve growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9212
Polymers35,4291
Non-polymers4921
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.915, 51.915, 229.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-950-

HOH

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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: 35428.723 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK1, MTC, TRK, TRKA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04629, receptor protein-tyrosine kinase
#2: Chemical ChemComp-OOJ / N-(5-{[(7-methyl-4-oxo-4H-pyrido[1,2-a]pyrimidin-2-yl)methyl]sulfanyl}-1,3,4-thiadiazol-2-yl)-N'-[3-(trifluoromethyl)phenyl]urea


Mass: 492.497 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15F3N6O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 20mM Tris/HCl, pH=8.5, 50mM NaCl, 2mM DTT, 0.5mM PMSF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→76.44 Å / Num. obs: 23189 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 22.51
Reflection shellResolution: 2.03→2.27 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.441 / % possible all: 95.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0049refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.331 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26029 1815 7.8 %RANDOM
Rwork0.21688 ---
obs0.22008 21335 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.938 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.03→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 33 57 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192375
X-RAY DIFFRACTIONr_bond_other_d0.0010.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9713237
X-RAY DIFFRACTIONr_angle_other_deg2.57835126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2265295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20723.0399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1731515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212725
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02565
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7385.8841177
X-RAY DIFFRACTIONr_mcbond_other4.7375.8821176
X-RAY DIFFRACTIONr_mcangle_it5.7169.9051473
X-RAY DIFFRACTIONr_mcangle_other5.7159.9091474
X-RAY DIFFRACTIONr_scbond_it5.8146.4271196
X-RAY DIFFRACTIONr_scbond_other5.8116.4281197
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.29710.6171764
X-RAY DIFFRACTIONr_long_range_B_refined8.24426.5422641
X-RAY DIFFRACTIONr_long_range_B_other8.24126.5282631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.083 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 151 -
Rwork0.317 1590 -
obs--99.49 %

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