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- PDB-6pma: TRK-A IN COMPLEX WITH LIGAND -

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Basic information

Entry
Database: PDB / ID: 6pma
TitleTRK-A IN COMPLEX WITH LIGAND
ComponentsHigh affinity nerve growth factor receptor
KeywordsTRANSFERASE / TRK-A KINASE DOMAIN
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 / Signalling to RAS / 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 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
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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-OQS / High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.53 Å
AuthorsSubramanian, G. / Brown, D.G.
CitationJournal: Rsc Med Chem / Year: 2020
Title: Synthetic inhibitor leads of human tropomyosin receptor kinase A ( h TrkA).
Authors: Subramanian, G. / Vairagoundar, R. / Bowen, S.J. / Roush, N. / Zachary, T. / Javens, C. / Williams, T. / Janssen, A. / Gonzales, A.
History
DepositionJul 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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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)35,9072
Polymers35,4291
Non-polymers4781
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.094, 52.094, 227.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK1, MTC, TRK, TRKA / Production host: Escherichia coli (E. coli)
References: UniProt: P04629, receptor protein-tyrosine kinase
#2: Chemical ChemComp-OQS / N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[1-(4-methoxyphenyl)-4-oxo-1,4-dihydro-5H-pyrazolo[3,4-d]pyrimidin-5-yl]acetamide


Mass: 477.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15ClF3N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).

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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 PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→75.72 Å / Num. obs: 12146 / % possible obs: 97.2 % / Redundancy: 4.2 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.51→2.76 Å / Redundancy: 4.3 % / Num. unique obs: 2755 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.53→45.16 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.57 / ESU R Free: 0.314
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 906 7.5 %RANDOM
Rwork0.2045 ---
obs0.2091 11226 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.42 Å2 / Biso mean: 41.149 Å2 / Biso min: 23.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----1.31 Å2
Refinement stepCycle: final / Resolution: 2.53→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 33 25 2381
Biso mean--38.34 46.97 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132338
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172161
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.6373178
X-RAY DIFFRACTIONr_angle_other_deg2.3851.5684963
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07920.973113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75215356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1781516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022617
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02515
X-RAY DIFFRACTIONr_mcbond_it3.2634.4641157
X-RAY DIFFRACTIONr_mcbond_other3.2644.4631156
X-RAY DIFFRACTIONr_mcangle_it5.2556.6811441
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 58 -
Rwork0.307 819 -
all-877 -
obs--96.48 %

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