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- PDB-4d58: Focal Adhesion Kinase catalytic domain in complex with bis-anilin... -

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Basic information

Entry
Database: PDB / ID: 4d58
TitleFocal Adhesion Kinase catalytic domain in complex with bis-anilino pyrimidine inhibitor
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 / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / calcium-dependent cysteine-type endopeptidase activity / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Integrin signaling ...Apoptotic cleavage of cellular proteins / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / radial glia-guided pyramidal neuron migration / negative regulation of protein autophosphorylation / 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 / angiogenesis involved in wound healing / signal complex assembly / response to pH / negative regulation of cell-substrate adhesion / wound healing, spreading of cells / positive regulation of focal adhesion assembly / positive regulation of protein tyrosine kinase activity / negative regulation of anoikis / regulation of cell adhesion / response to muscle stretch / ciliary basal body / molecular function activator activity / actin filament organization / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / sarcolemma / integrin binding / positive regulation of protein binding / cell cortex / protein tyrosine kinase activity / protease binding / protein autophosphorylation / dendritic spine / positive regulation of cell migration / focal adhesion / centrosome / positive regulation of cell population proliferation / 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. / Tyrosine-protein kinase, active site / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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
Chem-BI9 / Focal adhesion kinase 1
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 3, 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)64,2216
Polymers63,4642
Non-polymers7574
Water3,333185
1
A: FOCAL ADHESION KINASE


Theoretical massNumber of molelcules
Total (without water)31,7321
Polymers31,7321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FOCAL ADHESION KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4895
Polymers31,7321
Non-polymers7574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.983, 123.368, 50.843
Angle α, β, γ (deg.)90.00, 94.65, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BI9 / 2-({5-CHLORO-2-[(2-METHOXY-4-MORPHOLIN-4-YLPHENYL)AMINO]PYRIMIDIN-4-YL}AMINO)-N-METHYLBENZAMIDE


Mass: 468.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25ClN6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.22 Å3/Da / Density % sol: 44.59 % / 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: 1.95→61.68 Å / Num. obs: 40150 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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: 1.95→61.68 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.4 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22848 2030 5.1 %RANDOM
Rwork0.19556 ---
obs0.19725 38091 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.83 Å2
2--0.71 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 48 185 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194311
X-RAY DIFFRACTIONr_bond_other_d0.0020.024161
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9785834
X-RAY DIFFRACTIONr_angle_other_deg0.8173.0029574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2015518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23823.281192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35415775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3071535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 136 -
Rwork0.271 2767 -
obs--99.79 %
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)
11.1925-0.72910.15711.333-0.64732.5765-0.12080.0690.02080.12880.0356-0.15690.07820.04960.08520.0382-0.00920.02270.0235-0.03860.101531.512833.957716.7262
21.19690.31240.06720.9156-0.44631.4652-0.05320.1172-0.0804-0.05940.04980.04110.1464-0.14690.00350.0197-0.02390.01610.0333-0.02780.074814.033839.4404-1.864
30.6602-0.4804-0.60711.5737-0.68793.4627-0.0643-0.1080.0860.26720.0839-0.2362-0.21340.4838-0.01960.1101-0.0571-0.03120.1436-0.04260.093626.07415.789332.7172
41.1064-0.20080.38221.35190.12492.00840.0383-0.1215-0.01520.03190.0410.1057-0.1848-0.1569-0.07940.04-0.00040.03770.03260.00230.072510.32514.188312.5668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A414 - 503
2X-RAY DIFFRACTION2A504 - 684
3X-RAY DIFFRACTION3B415 - 503
4X-RAY DIFFRACTION4B504 - 685

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