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- PDB-4d4v: Focal Adhesion Kinase catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4d4v
TitleFocal Adhesion Kinase catalytic domain
ComponentsFOCAL ADHESION KINASE
KeywordsTRANSFERASE / FOCAL ADHESION KINASE / KINASE INHIBITOR / ATP-BINDING / INTEGRIN SIGNALING
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / negative regulation of protein autophosphorylation / radial glia-guided pyramidal neuron migration / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / signal complex assembly / response to pH / angiogenesis involved in wound healing / wound healing, spreading of cells / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / negative regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of protein binding / regulation of cell adhesion / response to muscle stretch / molecular function activator activity / actin filament organization / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / sarcolemma / integrin binding / epidermal growth factor receptor signaling pathway / protein autophosphorylation / protease binding / protein tyrosine kinase activity / cell cortex / positive regulation of cell migration / ciliary basal body / focal adhesion / positive regulation of cell population proliferation / centrosome / perinuclear region of cytoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / 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 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
Chem-KB8 / Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLe Coq, J. / Lin, A. / Lietha, D.
CitationJournal: Biophys.J. / Year: 2015
Title: Allosteric Regulation of Focal Adhesion Kinase by Pip2 and ATP.
Authors: Zhou, J. / Bronowska, A. / Le Coq, J. / Lietha, D. / Grater, F.
History
DepositionOct 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: FOCAL ADHESION KINASE
B: FOCAL ADHESION KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,37810
Polymers63,4642
Non-polymers9148
Water2,414134
1
A: FOCAL ADHESION KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9844
Polymers31,7321
Non-polymers2523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3936
Polymers31,7321
Non-polymers6625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.996, 123.597, 51.008
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FOCAL ADHESION KINASE / FADK 1 / FOCAL ADHESION KINASE-RELATED NONKINASE / FRNK / P41/P43FRNK / PROTEIN-TYROSINE KINASE 2 / ...FADK 1 / FOCAL ADHESION KINASE-RELATED NONKINASE / FRNK / P41/P43FRNK / PROTEIN-TYROSINE KINASE 2 / P125FAK / PP125FAK


Mass: 31731.805 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 411-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PACG2T / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-KB8 / 6-methyl-4-(piperazin-1-yl)-2-(trifluoromethyl)quinoline


Mass: 295.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16F3N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.23 Å3/Da / Density % sol: 44.9 % / Description: NONE
Crystal growDetails: 100 MM TRIS PH 8.5, 75 MM LISO4, 22% PEG4000, 10 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.1→50.85 Å / Num. obs: 32413 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKK

2jkk


Resolution: 2.1→50.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.652 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22704 1647 5.1 %RANDOM
Rwork0.19184 ---
obs0.19365 30740 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.727 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 53 134 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194245
X-RAY DIFFRACTIONr_bond_other_d0.0050.024110
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9775740
X-RAY DIFFRACTIONr_angle_other_deg0.7923.0039452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99923.298188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261534
X-RAY DIFFRACTIONr_chiral_restr0.0650.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7222.6442040
X-RAY DIFFRACTIONr_mcbond_other1.7222.6432039
X-RAY DIFFRACTIONr_mcangle_it2.7093.9452543
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0023.0462205
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.29 127 -
Rwork0.239 2280 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4154-0.2871-0.82892.0775-0.89145.5667-0.0318-0.14990.07790.51830.0485-0.2873-0.37460.6144-0.01680.3133-0.1045-0.01570.276-0.05580.237522.3936.07683.631
21.8513-0.25810.63411.5002-0.76452.1847-0.02830.1547-0.17610.01540.03010.02320.1283-0.0832-0.00170.0881-0.04060.08910.0346-0.04770.111215.83937.83955.458
32.7351-0.32780.83792.85770.02513.28820.0117-0.19410.08190.03650.10540.3422-0.2991-0.2142-0.1170.0896-0.00660.07270.0379-0.00450.10236.5844.58363.155
40000000000000000.0962000.096200.0962000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B415 - 503
2X-RAY DIFFRACTION2A415 - 686
3X-RAY DIFFRACTION3B504 - 686
4X-RAY DIFFRACTION4A504 - 686

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