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- PDB-3fzt: Crystal structure of PYK2 complexed with PF-4618433 -

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Basic information

Entry
Database: PDB / ID: 3fzt
TitleCrystal structure of PYK2 complexed with PF-4618433
ComponentsProtein tyrosine kinase 2 beta
KeywordsTRANSFERASE / PYK2 / Kinase / DFG / Alternative splicing / ATP-binding / Cell membrane / Cytoplasm / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Tyrosine-protein kinase
Function / homology
Function and homology information


regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / endothelin receptor signaling pathway ...regulation of macrophage chemotaxis / response to cation stress / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / 3-phosphoinositide-dependent protein kinase binding / regulation of ubiquitin-dependent protein catabolic process / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / apical dendrite / negative regulation of muscle cell apoptotic process / negative regulation of bone mineralization / cortical cytoskeleton organization / activation of Janus kinase activity / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / Interleukin-2 signaling / long-term synaptic depression / sprouting angiogenesis / NMDA selective glutamate receptor complex / oocyte maturation / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / stress fiber assembly / negative regulation of potassium ion transport / RHOU GTPase cycle / positive regulation of excitatory postsynaptic potential / response to immobilization stress / postsynaptic density, intracellular component / positive regulation of protein kinase activity / glutamate receptor binding / glial cell proliferation / cellular defense response / regulation of cell adhesion / bone resorption / vascular endothelial growth factor receptor signaling pathway / response to glucose / response to mechanical stimulus / peptidyl-tyrosine autophosphorylation / cellular response to retinoic acid / tumor necrosis factor-mediated signaling pathway / response to cAMP / ionotropic glutamate receptor signaling pathway / positive regulation of endothelial cell migration / response to hormone / positive regulation of synaptic transmission, glutamatergic / response to cocaine / positive regulation of translation / integrin-mediated signaling pathway / response to ischemia / long-term synaptic potentiation / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / positive regulation of JNK cascade / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / response to hydrogen peroxide / regulation of synaptic plasticity / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / positive regulation of nitric oxide biosynthetic process / MAPK cascade / neuron projection development / lamellipodium / presynapse / regulation of cell shape / cell cortex / positive regulation of cytosolic calcium ion concentration / growth cone / cell body / positive regulation of cell growth / protein tyrosine kinase activity / protein-containing complex assembly / response to ethanol / negative regulation of neuron apoptotic process / protein autophosphorylation / adaptive immune response / dendritic spine / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / cell surface receptor signaling pathway / response to hypoxia / positive regulation of cell migration
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. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Chem-4JZ / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein tyrosine kinase 2 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6362
Polymers32,1901
Non-polymers4461
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.713, 82.915, 86.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-4JZ / 1-[5-tert-butyl-2-(4-methylphenyl)-1,2-dihydro-3H-pyrazol-3-ylidene]-3-{3-[(pyridin-3-yloxy)methyl]-1H-pyrazol-5-yl}urea


Mass: 445.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 295 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 295K

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Data collection

DiffractionMean temperature: 100 K
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: 1.95→30 Å / Num. obs: 19176 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1525 / % possible all: 75.8

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Processing

SoftwareName: REFMAC / Version: 5.3.0008 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.416 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 979 5.1 %RANDOM
Rwork0.196 ---
obs0.19833 18100 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.455 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.42 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 33 196 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222185
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9892958
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3145256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15224.16796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18915393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1261512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021631
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.21030
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21506
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8631.51342
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37822103
X-RAY DIFFRACTIONr_scbond_it2.1423987
X-RAY DIFFRACTIONr_scangle_it3.1694.5855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 46 -
Rwork0.187 1011 -
obs--70.23 %

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