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- PDB-1mp8: Crystal structure of Focal Adhesion Kinase (FAK) -

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Basic information

Entry
Database: PDB / ID: 1mp8
TitleCrystal structure of Focal Adhesion Kinase (FAK)
Componentsfocal adhesion kinase 1
KeywordsTRANSFERASE / tyrosine protein kinase
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / positive regulation of ubiquitin-dependent protein catabolic process / JUN kinase binding / signal complex assembly / positive regulation of macrophage proliferation / positive regulation of fibroblast migration / DCC mediated attractive signaling / growth hormone receptor signaling pathway / Signal regulatory protein family interactions / regulation of GTPase activity / MET activates PTK2 signaling / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / positive regulation of wound healing / regulation of osteoblast differentiation / p130Cas linkage to MAPK signaling for integrins / establishment of cell polarity / Apoptotic cleavage of cellular proteins / positive regulation of macrophage chemotaxis / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / Fc-gamma receptor signaling pathway involved in phagocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / positive regulation of epithelial cell migration / ephrin receptor signaling pathway / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of protein kinase activity / RHO GTPases Activate WASPs and WAVEs / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / regulation of protein phosphorylation / heart morphogenesis / positive regulation of epithelial to mesenchymal transition / stress fiber / EPHB-mediated forward signaling / protein tyrosine phosphatase activity / Integrin signaling / NCAM signaling for neurite out-growth / SH2 domain binding / transforming growth factor beta receptor signaling pathway / axon guidance / ciliary basal body / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / FCGR3A-mediated phagocytosis / placenta development / cell motility / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / peptidyl-tyrosine phosphorylation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cell migration / integrin binding / regulation of cell shape / actin binding / regulation of cell population proliferation / cell cortex / protein tyrosine kinase activity / RAF/MAP kinase cascade / protein autophosphorylation / protein phosphatase binding / angiogenesis / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / dendritic spine / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / intracellular membrane-bounded organelle / focal adhesion / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / ATP binding / nucleus / plasma membrane / cytosol
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 domain signature 2. / FERM central domain ...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 domain signature 2. / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE-5'-DIPHOSPHATE / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNowakowski, J. / Cronin, C.N. / McRee, D.E. / Knuth, M.W. / Nelson, C.G. / Pavletich, N.P. / Rodgers, J. / Sang, B.-C. / Scheibe, D.N. / Swanson, R.V. / Thompson, D.A.
CitationJournal: Structure / Year: 2002
Title: Structures of the cancer-related Aurora-A, FAK, and EphA2 protein kinases from nanovolume crystallography
Authors: Nowakowski, J. / Cronin, C.N. / McRee, D.E. / Knuth, M.W. / Nelson, C.G. / Pavletich, N.P. / Rodgers, J. / Sang, B.-C. / Scheibe, D.N. / Swanson, R.V. / Thompson, D.A.
History
DepositionSep 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5472
Polymers32,1201
Non-polymers4271
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.189, 46.636, 62.225
Angle α, β, γ (deg.)90.00, 80.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein focal adhesion kinase 1 / fak / fadk 1 / pp125fak / protein-tyrosine kinase 2


Mass: 32120.139 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAK / Cell line (production host): Hi 5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05397, EC: 2.7.1.112
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 2000, citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.1 mg/mlprotein1drop
250 mMTris-HCl1droppH7.6
3250 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
60.1 Mcitrate/acetate1reservoirpH5.
724 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 2002
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46 Å / Num. all: 33856 / Num. obs: 25589 / % possible obs: 75.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.6→1.7 Å / % possible all: 50
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 24650 / % possible obs: 91.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 65 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.691 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.23025 1305 5.1 %RANDOM
Rwork0.17922 ---
all0.188 33856 --
obs0.18182 24202 75.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-1.02 Å2
2---0.56 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2018 0 27 233 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222092
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9742834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2193249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.95315400
X-RAY DIFFRACTIONr_chiral_restr0.1170.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021545
X-RAY DIFFRACTIONr_nbd_refined0.2480.31094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.516
X-RAY DIFFRACTIONr_mcbond_it1.0311.51258
X-RAY DIFFRACTIONr_mcangle_it1.89422037
X-RAY DIFFRACTIONr_scbond_it3.1463834
X-RAY DIFFRACTIONr_scangle_it5.0884.5797
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 34
Rwork0.229 592
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Num. reflection obs: 22650 / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.66

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