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- PDB-8xox: The Crystal Structure of FAK2 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xox
TitleThe Crystal Structure of FAK2 from Biortus.
ComponentsProtein-tyrosine kinase 2-beta
KeywordsTRANSFERASE / Kinase / Adaptive immunity / ATP-binding
Function / homology
Function and homology information


regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly ...regulation of macrophage chemotaxis / neurotransmitter receptor regulator activity / positive regulation of B cell chemotaxis / marginal zone B cell differentiation / regulation of ubiquitin-dependent protein catabolic process / endothelin receptor signaling pathway / negative regulation of myeloid cell differentiation / negative regulation of bone mineralization / cortical cytoskeleton organization / regulation of postsynaptic density assembly / activation of Janus kinase activity / chemokine-mediated signaling pathway / apical dendrite / cellular response to fluid shear stress / regulation of release of sequestered calcium ion into cytosol / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / calcium/calmodulin-dependent protein kinase activity / sprouting angiogenesis / Interleukin-2 signaling / Signal regulatory protein family interactions / NMDA selective glutamate receptor complex / peptidyl-tyrosine autophosphorylation / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / Golgi organization / negative regulation of potassium ion transport / positive regulation of protein kinase activity / RHOU GTPase cycle / signaling receptor activator activity / positive regulation of excitatory postsynaptic potential / vascular endothelial growth factor receptor signaling pathway / bone resorption / positive regulation of synaptic transmission, glutamatergic / postsynaptic density, intracellular component / cellular defense response / regulation of cell adhesion / cellular response to retinoic acid / ionotropic glutamate receptor binding / positive regulation of endothelial cell migration / ionotropic glutamate receptor signaling pathway / peptidyl-tyrosine phosphorylation / tumor necrosis factor-mediated signaling pathway / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / non-membrane spanning protein tyrosine kinase activity / positive regulation of JNK cascade / non-specific protein-tyrosine kinase / positive regulation of neuron projection development / regulation of synaptic plasticity / VEGFA-VEGFR2 Pathway / long-term synaptic potentiation / epidermal growth factor receptor signaling pathway / neuron migration / positive regulation of angiogenesis / presynapse / lamellipodium / regulation of cell shape / growth cone / cell body / protein autophosphorylation / protein-containing complex assembly / protein tyrosine kinase activity / cell cortex / adaptive immune response / negative regulation of neuron apoptotic process / cytoskeleton / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / positive regulation of cell migration / negative regulation of cell population proliferation / focal adhesion / neuronal cell body / positive regulation of cell population proliferation / apoptotic process / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-YAM / Protein-tyrosine kinase 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of FAK2 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Wang, J.
History
DepositionJan 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-tyrosine kinase 2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8845
Polymers32,1901
Non-polymers6944
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint1 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.797, 59.132, 67.295
Angle α, β, γ (deg.)90.000, 95.033, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32190.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2B, FAK2, PYK2, RAFTK / Production host: Escherichia coli (E. coli)
References: UniProt: Q14289, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-YAM / N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide


Mass: 507.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20F3N7O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M LiCl2, 0.1M Tris pH8.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.9→44.384 Å / Num. obs: 23394 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.701 / Num. unique obs: 1465

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.384 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.636 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2298 1141 4.881 %
Rwork0.1693 22237 -
all0.172 --
obs-23378 99.782 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.469 Å2
Baniso -1Baniso -2Baniso -3
1--1.822 Å2-0 Å2-1.269 Å2
2--1.868 Å20 Å2
3---0.175 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 47 207 2369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122240
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162147
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.663039
X-RAY DIFFRACTIONr_angle_other_deg0.481.5774964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.9939.68816
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg12.534203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91110404
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.8791097
X-RAY DIFFRACTIONr_chiral_restr0.0680.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022557
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_nbd_refined0.2140.2469
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21991
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21107
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21181
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2156
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.217
X-RAY DIFFRACTIONr_nbd_other0.1980.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.210
X-RAY DIFFRACTIONr_mcbond_it2.682.6931052
X-RAY DIFFRACTIONr_mcbond_other2.6742.6921052
X-RAY DIFFRACTIONr_mcangle_it3.6344.8211314
X-RAY DIFFRACTIONr_mcangle_other3.6364.8241315
X-RAY DIFFRACTIONr_scbond_it4.0453.2621188
X-RAY DIFFRACTIONr_scbond_other4.0443.2641189
X-RAY DIFFRACTIONr_scangle_it6.4415.7221720
X-RAY DIFFRACTIONr_scangle_other6.4395.7231721
X-RAY DIFFRACTIONr_lrange_it7.71931.5732644
X-RAY DIFFRACTIONr_lrange_other7.730.312582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.283760.2611626X-RAY DIFFRACTION98.2112
1.949-2.0030.296800.2261595X-RAY DIFFRACTION99.8807
2.003-2.0610.297790.2081538X-RAY DIFFRACTION100
2.061-2.1240.249740.1881519X-RAY DIFFRACTION100
2.124-2.1930.228720.1871454X-RAY DIFFRACTION99.9345
2.193-2.270.269930.1781377X-RAY DIFFRACTION100
2.27-2.3560.249570.1711404X-RAY DIFFRACTION100
2.356-2.4510.232600.1621291X-RAY DIFFRACTION100
2.451-2.560.226680.1631275X-RAY DIFFRACTION99.9256
2.56-2.6850.257660.1651215X-RAY DIFFRACTION99.922
2.685-2.8290.242590.171144X-RAY DIFFRACTION100
2.829-30.313410.1731079X-RAY DIFFRACTION99.6441
3-3.2060.207470.1681052X-RAY DIFFRACTION99.9091
3.206-3.4620.206550.169942X-RAY DIFFRACTION99.6004
3.462-3.790.166440.158886X-RAY DIFFRACTION99.8926
3.79-4.2330.219530.151786X-RAY DIFFRACTION99.881
4.233-4.8810.22400.132700X-RAY DIFFRACTION100
4.881-5.960.236410.164594X-RAY DIFFRACTION99.8428
5.96-8.3530.205210.171475X-RAY DIFFRACTION99.7988

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