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- PDB-5d7v: Crystal structure of PTK6 kinase domain -

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Basic information

Entry
Database: PDB / ID: 5d7v
TitleCrystal structure of PTK6 kinase domain
ComponentsProtein-tyrosine kinase 6Tyrosine kinase
KeywordsTRANSFERASE / KINASE / BRK / APO
Function / homology
Function and homology information


PTK6 Activates STAT3 / negative regulation of protein tyrosine kinase activity / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / tyrosine phosphorylation of STAT protein / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 promotes HIF1A stabilization ...PTK6 Activates STAT3 / negative regulation of protein tyrosine kinase activity / PTK6 Regulates Proteins Involved in RNA Processing / intestinal epithelial cell differentiation / ERBB2 signaling pathway / negative regulation of growth / PTK6 Expression / tyrosine phosphorylation of STAT protein / positive regulation of epidermal growth factor receptor signaling pathway / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / PTK6 Down-Regulation / PTK6 Regulates Cell Cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / ruffle / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of DNA replication / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Cytoprotection by HMOX1 / SCF(Skp2)-mediated degradation of p27/p21 / positive regulation of neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / Cyclin D associated events in G1 / cell migration / protein tyrosine kinase activity / protein autophosphorylation / cell differentiation / nuclear body / protein phosphorylation / signaling receptor binding / innate immune response / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PTK6, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...PTK6, SH2 domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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
PHOSPHATE ION / Protein-tyrosine kinase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
Model detailsTRANSFERASE
AuthorsThakur, M.K. / Birudukota, S. / Swaminathan, S. / Tyagi, R. / Gosu, R.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Crystal structure of the kinase domain of human protein tyrosine kinase 6 (PTK6) at 2.33 angstrom resolution
Authors: Thakur, M.K. / Kumar, A. / Birudukota, S. / Swaminathan, S. / Tyagi, R. / Gosu, R.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine kinase 6
B: Protein-tyrosine kinase 6
C: Protein-tyrosine kinase 6
D: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,04920
Polymers124,5644
Non-polymers1,48516
Water6,593366
1
A: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5125
Polymers31,1411
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-2 kcal/mol
Surface area13060 Å2
MethodPISA
2
B: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5125
Polymers31,1411
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12410 Å2
MethodPISA
3
C: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5125
Polymers31,1411
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12710 Å2
MethodPISA
4
D: Protein-tyrosine kinase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5125
Polymers31,1411
Non-polymers3714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-1 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.718, 76.308, 87.271
Angle α, β, γ (deg.)81.460, 75.920, 74.930
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein-tyrosine kinase 6 / Tyrosine kinase / Breast tumor kinase / Tyrosine-protein kinase BRK


Mass: 31140.910 Da / Num. of mol.: 4 / Fragment: PTK6_KINASE DOMAIN, UNP residues 185-446 / Mutation: C433T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK6 / Plasmid: pFastBac1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13882, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.23M Diammonium Phosphate, 18% PEG 3350, 1M Lithium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54789 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2015 / Details: VariMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54789 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. obs: 50742 / % possible obs: 96.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 7.3
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F4J

2f4j


Resolution: 2.33→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 9.7 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 2476 5.1 %RANDOM
Rwork0.2186 ---
obs0.2218 46364 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.01 Å2 / Biso mean: 26.633 Å2 / Biso min: 11.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å2-0.49 Å20.87 Å2
2---0.61 Å2-0.29 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8592 0 92 366 9050
Biso mean--41.16 26.63 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218992
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.96612147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81351076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40122.99418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.169151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6441571
X-RAY DIFFRACTIONr_chiral_restr0.0830.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026713
X-RAY DIFFRACTIONr_nbd_refined0.1970.24319
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2529
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.2143
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.220
X-RAY DIFFRACTIONr_mcbond_it0.3871.55529
X-RAY DIFFRACTIONr_mcangle_it0.68928649
X-RAY DIFFRACTIONr_scbond_it0.92233939
X-RAY DIFFRACTIONr_scangle_it1.4914.53484
LS refinement shellResolution: 2.334→2.394 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 158 -
Rwork0.284 3252 -
all-3410 -
obs--90.38 %

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