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- PDB-3fzo: Crystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase -

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Basic information

Entry
Database: PDB / ID: 3fzo
TitleCrystal Structure of PYK2-Apo, Proline-rich Tyrosine Kinase
ComponentsProtein tyrosine kinase 2 beta
KeywordsTRANSFERASE / tyrosine kinase / dfg-out / Alternative splicing / ATP-binding / Cell membrane / Cytoplasm / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Tyrosine-protein kinase
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / regulation of postsynaptic density assembly / blood vessel endothelial cell migration / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / apical dendrite / positive regulation of ubiquitin-dependent protein catabolic process / regulation of release of sequestered calcium ion into cytosol / activation of Janus kinase activity / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Interleukin-2 signaling / sprouting angiogenesis / oocyte maturation / long-term synaptic depression / regulation of NMDA receptor activity / calmodulin-dependent protein kinase activity / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / negative regulation of potassium ion transport / positive regulation of excitatory postsynaptic potential / RHOU GTPase cycle / response to immobilization stress / positive regulation of protein kinase activity / postsynaptic density, intracellular component / glial cell proliferation / cellular defense response / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of synaptic transmission, glutamatergic / response to cocaine / response to hormone / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Schaffer collateral - CA1 synapse / regulation of synaptic plasticity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / response to calcium ion / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / neuron projection development / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / presynapse / lamellipodium / cell cortex / cell body / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / growth cone / positive regulation of cell growth / protein-containing complex assembly / protein tyrosine kinase activity / response to ethanol / adaptive immune response / negative regulation of neuron apoptotic process / dendritic spine / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / cytoskeleton
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / 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
Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHan, S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural characterization of proline-rich tyrosine kinase 2 (PYK2) reveals a unique (DFG-out) conformation and enables inhibitor design.
Authors: Han, S. / Mistry, A. / Chang, J.S. / Cunningham, D. / Griffor, M. / Bonnette, P.C. / Wang, H. / Chrunyk, B.A. / Aspnes, G.E. / Walker, D.P. / Brosius, A.D. / Buckbinder, L.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein tyrosine kinase 2 beta


Theoretical massNumber of molelcules
Total (without water)32,1901
Polymers32,1901
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.284, 96.976, 43.066
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein tyrosine kinase 2 beta / Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Cell adhesion kinase beta / CAK ...Focal adhesion kinase 2 / FADK 2 / Proline-rich tyrosine kinase 2 / Cell adhesion kinase beta / CAK beta / Calcium-dependent tyrosine kinase / CADTK / Related adhesion focal tyrosine kinase / RAFTK


Mass: 32190.320 Da / Num. of mol.: 1 / Fragment: UNP residues 416-692, Protein kinase domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 0.2M MgCl2, 20-27% PEG3350, 1mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 15582 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.41 / Num. unique all: 1553 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MP8

1mp8


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.883 / SU B: 6.61 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26539 778 5 %RANDOM
Rwork0.20367 ---
obs0.2067 14747 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.211 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-0.06 Å2
2--1.09 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 0 128 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222179
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9712949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2035260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61424.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36415399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5161512
X-RAY DIFFRACTIONr_chiral_restr0.110.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021615
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2990
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21490
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.51365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63222131
X-RAY DIFFRACTIONr_scbond_it2.1983961
X-RAY DIFFRACTIONr_scangle_it3.4094.5818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 65 -
Rwork0.237 1080 -
obs--99.83 %

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