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- PDB-3fzp: Crystal structure of PYK2 complexed with ATPgS -

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Basic information

Entry
Database: PDB / ID: 3fzp
TitleCrystal structure of PYK2 complexed with ATPgS
ComponentsProtein tyrosine kinase 2 beta
KeywordsTRANSFERASE / Kinase / ATPgS / 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 / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration ...regulation of macrophage chemotaxis / response to cation stress / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / 3-phosphoinositide-dependent protein kinase binding / endothelin receptor signaling pathway / regulation of postsynaptic density assembly / negative regulation of myeloid cell differentiation / blood vessel endothelial cell migration / negative regulation of bone mineralization / negative regulation of muscle cell apoptotic process / cortical cytoskeleton organization / apical dendrite / oocyte maturation / positive regulation of ubiquitin-dependent protein catabolic process / activation of Janus kinase activity / regulation of release of sequestered calcium ion into cytosol / cellular response to fluid shear stress / focal adhesion assembly / signal complex assembly / chemokine-mediated signaling pathway / calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / sprouting angiogenesis / Interleukin-2 signaling / long-term synaptic depression / positive regulation of cell-matrix adhesion / Signal regulatory protein family interactions / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / positive regulation of actin filament polymerization / stress fiber assembly / postsynaptic density, intracellular component / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / negative regulation of potassium ion transport / RHOU GTPase cycle / response to immobilization stress / positive regulation of protein kinase activity / glial cell proliferation / cellular defense response / response to glucose / vascular endothelial growth factor receptor signaling pathway / response to mechanical stimulus / regulation of cell adhesion / cellular response to retinoic acid / peptidyl-tyrosine autophosphorylation / bone resorption / response to cAMP / tumor necrosis factor-mediated signaling pathway / ionotropic glutamate receptor signaling pathway / response to hormone / positive regulation of synaptic transmission, glutamatergic / positive regulation of endothelial cell migration / positive regulation of translation / response to cocaine / long-term synaptic potentiation / integrin-mediated signaling pathway / response to ischemia / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / regulation of synaptic plasticity / non-specific protein-tyrosine kinase / Schaffer collateral - CA1 synapse / non-membrane spanning protein tyrosine kinase activity / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / positive regulation of neuron projection development / VEGFA-VEGFR2 Pathway / response to calcium ion / peptidyl-tyrosine phosphorylation / neuron projection development / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / : / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-tyrosine phosphorylation / presynapse / lamellipodium / cell body / cell cortex / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / growth cone / positive regulation of cell growth / protein-containing complex assembly / protein tyrosine kinase activity / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / postsynaptic density / adaptive immune response / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 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)32,9064
Polymers32,1901
Non-polymers7153
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.946, 92.663, 42.671
Angle α, β, γ (deg.)90.00, 92.45, 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: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Citrate, 0.5-1.5M Lithium Sulfate, 0.2-0.4M Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 15837 / % possible obs: 94.1 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1527 / % possible all: 90.5

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.401 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23898 802 5.1 %RANDOM
Rwork0.21071 ---
obs0.21227 14989 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.727 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.77 Å2
2---1.58 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 41 105 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222188
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9922969
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20224.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.54715393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6041512
X-RAY DIFFRACTIONr_chiral_restr0.1470.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021602
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.2998
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21459
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.287
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.051.51343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72622104
X-RAY DIFFRACTIONr_scbond_it2.2483996
X-RAY DIFFRACTIONr_scangle_it3.4554.5865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 51 -
Rwork0.234 1080 -
obs--90.77 %

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