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- PDB-4d5k: Focal Adhesion Kinase catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4d5k
TitleFocal Adhesion Kinase catalytic domain
ComponentsFOCAL ADHESION KINASE
KeywordsTRANSFERASE / 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 / actin filament organization / molecular function activator activity / 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 / ciliary basal body / positive regulation of cell migration / 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
Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionNov 5, 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)63,9267
Polymers63,4642
Non-polymers4625
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-43 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.930, 122.852, 50.875
Angle α, β, γ (deg.)90.00, 94.76, 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 / FOCAL ADHES ION KINASE


Mass: 31731.805 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, UNP 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 (butterflies/moths)
References: UniProt: Q00944, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.21 Å3/Da / Density % sol: 44.32 % / Description: NONE
Crystal growDetails: 100 MM TRIS PH 8.5, 75 MM LISO4, 24% PEG4000, 10 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS / 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: 1.75→61.43 Å / Num. obs: 53963 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 9.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.3 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JKK

2jkk


Resolution: 1.75→61.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.792 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21437 2718 5 %RANDOM
Rwork0.18906 ---
obs0.19035 51212 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20.78 Å2
2---0.5 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→61.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4109 0 24 218 4351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194284
X-RAY DIFFRACTIONr_bond_other_d0.0010.024169
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9735806
X-RAY DIFFRACTIONr_angle_other_deg0.77239609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.08123.263190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.011535
X-RAY DIFFRACTIONr_chiral_restr0.0780.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02982
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 177 -
Rwork0.293 3315 -
obs--86.26 %
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)
10.4398-0.0819-1.31271.5052-0.66625.09760.0468-0.27420.09820.48480.0352-0.2026-0.38380.5621-0.0820.2693-0.0671-0.03910.2978-0.06150.187970.8615.93132.844
22.0896-0.81130.13412.627-0.76052.7814-0.11570.0292-0.02930.2034-0.0176-0.27240.120.20210.13330.1028-0.02480.00340.0727-0.02440.115276.40233.83316.827
32.0647-0.40610.42562.3432-0.15462.39240.0473-0.16350.01850.03760.13180.3054-0.25-0.2595-0.17910.04130.01360.03450.04970.02220.062755.0094.55811.907
41.67180.6748-0.04662.0776-0.52832.5713-0.06620.1231-0.1029-0.10810.0270.1330.2849-0.26280.03920.0403-0.02380.01780.0505-0.00160.051758.91739.473-1.696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B415 - 503
2X-RAY DIFFRACTION2A415 - 503
3X-RAY DIFFRACTION3B504 - 686
4X-RAY DIFFRACTION4A504 - 686

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