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- PDB-6d22: Crystal structure of Tyrosine-protein kinase receptor -

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Basic information

Entry
Database: PDB / ID: 6d22
TitleCrystal structure of Tyrosine-protein kinase receptor
ComponentsTyrosine-protein kinase receptor
KeywordsTRANSFERASE / Allostric Inhibitor Tyrosine kinase
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 / cell surface receptor protein tyrosine kinase signaling pathway / 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 / nervous system development / 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 / cell differentiation / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase receptor / High affinity nerve growth factor receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.46 Å
AuthorsGreasley, S.E. / Brown, D.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Allosteric, Potent, Subtype Selective, and Peripherally Restricted TrkA Kinase Inhibitors.
Authors: Bagal, S.K. / Omoto, K. / Blakemore, D.C. / Bungay, P.J. / Bilsland, J.G. / Clarke, P.J. / Corbett, M.S. / Cronin, C.N. / Cui, J.J. / Dias, R. / Flanagan, N.J. / Greasley, S.E. / Grimley, R. ...Authors: Bagal, S.K. / Omoto, K. / Blakemore, D.C. / Bungay, P.J. / Bilsland, J.G. / Clarke, P.J. / Corbett, M.S. / Cronin, C.N. / Cui, J.J. / Dias, R. / Flanagan, N.J. / Greasley, S.E. / Grimley, R. / Johnson, E. / Fengas, D. / Kitching, L. / Kraus, M.L. / McAlpine, I. / Nagata, A. / Waldron, G.J. / Warmus, J.S.
History
DepositionApr 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 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.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase receptor


Theoretical massNumber of molelcules
Total (without water)34,9701
Polymers34,9701
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15300 Å2
2
A: Tyrosine-protein kinase receptor

A: Tyrosine-protein kinase receptor


Theoretical massNumber of molelcules
Total (without water)69,9412
Polymers69,9412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area2080 Å2
ΔGint-13 kcal/mol
Surface area28530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.120, 105.120, 203.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Tyrosine-protein kinase receptor


Mass: 34970.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTRK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: J3KP20, UniProt: P04629*PLUS, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 0.1M tri-Sodium citrate + 20% PEG3K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.458→19.906 Å / Num. obs: 15776 / % possible obs: 98.1 % / Redundancy: 5.7 % / Rpim(I) all: 0.066 / Rrim(I) all: 0.161 / Rsym value: 0.133 / Net I/av σ(I): 5.2 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.46-2.594.21.0730.720280.6411.3911.07388.4
2.59-2.755.60.910.821910.461.110.91100
2.75-2.945.80.6011.320770.2940.7190.601100
2.94-3.175.80.377219160.1890.4590.377100
3.17-3.486.20.2143.517970.1010.2540.214100
3.48-3.896.20.1086.916110.0510.1290.108100
3.89-4.496.20.06510.514410.030.0770.065100
4.49-5.56.20.05911.712190.0280.070.059100
5.5-7.776.10.0659.79650.0310.0770.065100
7.77-19.9065.60.04710.65310.0230.0560.04794.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
BUSTERphasing
RefinementResolution: 2.46→19.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.692 / SU ML: 0.168 / SU R Cruickshank DPI: 0.4334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.274 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 692 5 %RANDOM
Rwork0.1755 ---
obs0.1784 13113 79.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 100.52 Å2 / Biso mean: 37.404 Å2 / Biso min: 8.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å21.02 Å20 Å2
2--2.04 Å20 Å2
3----3.05 Å2
Refinement stepCycle: final / Resolution: 2.46→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2388 0 0 165 2553
Biso mean---45.7 -
Num. residues----299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0222448
X-RAY DIFFRACTIONr_angle_refined_deg2.7361.9563315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4275298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91822.5116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.40715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0911524
X-RAY DIFFRACTIONr_chiral_restr0.1810.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211878
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 47 -
Rwork0.27 948 -
all-995 -
obs--79.47 %

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