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- PDB-2ijm: Crystal Structure of Focal Adhesion Kinase Domain with 2 molecule... -

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Basic information

Entry
Database: PDB / ID: 2ijm
TitleCrystal Structure of Focal Adhesion Kinase Domain with 2 molecules in the Asymmetric Unit Complexed with ADP and ATP
ComponentsFocal Adhesion Kinase 1PTK2
KeywordsSIGNALING PROTEIN / TRANSFERASE / kinase catalytic domain
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 / Signal regulatory protein family interactions / growth hormone receptor signaling pathway / regulation of osteoblast differentiation / regulation of cytoskeleton organization / MET activates PTK2 signaling / regulation of focal adhesion assembly / establishment of cell polarity / positive regulation of wound healing / positive regulation of macrophage chemotaxis / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / p130Cas linkage to MAPK signaling for integrins / positive regulation of epithelial cell migration / negative regulation of cell-cell adhesion / Apoptotic cleavage of cellular proteins / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / positive regulation of epithelial to mesenchymal transition / ephrin receptor signaling pathway / positive regulation of protein kinase activity / vascular endothelial growth factor receptor signaling pathway / regulation of cell adhesion / heart morphogenesis / stress fiber / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / Integrin signaling / transforming growth factor beta receptor signaling pathway / ciliary basal body / placenta development / protein tyrosine phosphatase activity / molecular function activator activity / cell motility / integrin-mediated signaling pathway / axon guidance / FCGR3A-mediated phagocytosis / regulation of protein phosphorylation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell migration / integrin binding / actin binding / regulation of cell population proliferation / cell cortex / regulation of cell shape / RAF/MAP kinase cascade / protein phosphatase binding / angiogenesis / protein tyrosine kinase activity / dendritic spine / Extra-nuclear estrogen signaling / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / focal adhesion / intracellular membrane-bounded organelle / 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 / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.187 Å
AuthorsLee, C.C.
CitationJournal: To be Published
Title: Crystal Structure of Focal Adhesion Kinase Catalytic Domain Complexed with ATP and Novel 7H-Pyrrolo [2,3-d] pyrimidine Inhibitor Scaffolds
Authors: Andersen, C.B. / Ng, K. / Ficarro, S. / Vu, C. / Choi, H.-S. / He, Y. / Spraggon, G. / Gray, N. / Lee, C.C.
History
DepositionSep 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
B: Focal Adhesion Kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3974
Polymers64,4622
Non-polymers9342
Water3,315184
1
A: Focal Adhesion Kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7382
Polymers32,2311
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Focal Adhesion Kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6582
Polymers32,2311
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.432, 51.645, 66.544
Angle α, β, γ (deg.)99.81, 103.55, 90.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Focal Adhesion Kinase 1 / PTK2 / E.C.2.7.10.2 / FADK 1 / pp125FAK / Protein-tyrosine kinase 2


Mass: 32231.170 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (v/v) PEG-600, 10% glycerol, 0.1M HEPES pH 7.5, 0.05M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2003 / Details: CURVED SI (111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.187→34.3 Å / Num. all: 29887 / Num. obs: 28426 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.056 / Net I/σ(I): 16.3
Reflection shellResolution: 2.187→2.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2144 / Rsym value: 0.283 / % possible all: 70.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBA

1jba


Resolution: 2.187→34.3 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.484 / SU ML: 0.169 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27149 1436 5.1 %RANDOM
Rwork0.2073 ---
obs0.21051 26989 100 %-
all-26989 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.932 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.11 Å2-0.44 Å2
2--0.21 Å2-1.91 Å2
3----1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.187→34.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 58 184 4445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224360
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9825912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1755521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08323.434198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28415774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3411536
X-RAY DIFFRACTIONr_chiral_restr0.0920.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023256
X-RAY DIFFRACTIONr_nbd_refined0.2040.22179
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.223
X-RAY DIFFRACTIONr_mcbond_it0.7331.52699
X-RAY DIFFRACTIONr_mcangle_it1.22424237
X-RAY DIFFRACTIONr_scbond_it1.6331909
X-RAY DIFFRACTIONr_scangle_it2.6184.51675
LS refinement shellResolution: 2.187→2.244 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 81 -
Rwork0.252 1437 -
obs-1437 100 %

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