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- PDB-3bz3: Crystal Structure Analysis of Focal Adhesion Kinase with a Methan... -

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Basic information

Entry
Database: PDB / ID: 3bz3
TitleCrystal Structure Analysis of Focal Adhesion Kinase with a Methanesulfonamide Diaminopyrimidine Inhibitor
ComponentsFocal adhesion kinase 1
KeywordsTRANSFERASE / kinase / DFG-helix / Acetylation / Alternative splicing / ATP-binding / Cell junction / Nucleotide-binding / Phosphoprotein / 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 fibroblast migration / positive regulation of macrophage proliferation ...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 fibroblast migration / positive regulation of macrophage proliferation / DCC mediated attractive signaling / regulation of osteoblast differentiation / growth hormone receptor signaling pathway / Signal regulatory protein family interactions / MET activates PTK2 signaling / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of focal adhesion assembly / regulation of GTPase activity / positive regulation of wound healing / establishment of cell polarity / p130Cas linkage to MAPK signaling for integrins / negative regulation of cell-cell adhesion / positive regulation of macrophage chemotaxis / positive regulation of epithelial cell migration / Apoptotic cleavage of cellular proteins / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of anoikis / ephrin receptor signaling pathway / positive regulation of protein kinase activity / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / regulation of cell adhesion / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / positive regulation of epithelial to mesenchymal transition / stress fiber / EPHB-mediated forward signaling / Integrin signaling / NCAM signaling for neurite out-growth / SH2 domain binding / transforming growth factor beta receptor signaling pathway / ciliary basal body / protein tyrosine phosphatase activity / axon guidance / molecular function activator activity / integrin-mediated signaling pathway / cell motility / non-specific protein-tyrosine kinase / FCGR3A-mediated phagocytosis / non-membrane spanning protein tyrosine kinase activity / regulation of protein phosphorylation / epidermal growth factor receptor signaling pathway / placenta development / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / integrin binding / cell migration / regulation of cell shape / regulation of cell population proliferation / actin binding / cell cortex / RAF/MAP kinase cascade / protein tyrosine kinase activity / protein phosphatase binding / angiogenesis / protein autophosphorylation / Extra-nuclear estrogen signaling / dendritic spine / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoskeleton / positive regulation of cell migration / positive regulation of protein phosphorylation / 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 / 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-YAM / Focal adhesion kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsVajdos, F. / Marr, E.
CitationJournal: Cancer Res. / Year: 2008
Title: Antitumor activity and pharmacology of a selective focal adhesion kinase inhibitor, PF-562,271.
Authors: Roberts, W.G. / Ung, E. / Whalen, P. / Cooper, B. / Hulford, C. / Autry, C. / Richter, D. / Emerson, E. / Lin, J. / Kath, J. / Coleman, K. / Yao, L. / Martinez-Alsina, L. / Lorenzen, M. / ...Authors: Roberts, W.G. / Ung, E. / Whalen, P. / Cooper, B. / Hulford, C. / Autry, C. / Richter, D. / Emerson, E. / Lin, J. / Kath, J. / Coleman, K. / Yao, L. / Martinez-Alsina, L. / Lorenzen, M. / Berliner, M. / Luzzio, M. / Patel, N. / Schmitt, E. / LaGreca, S. / Jani, J. / Wessel, M. / Marr, E. / Griffor, M. / Vajdos, F.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2652
Polymers31,7581
Non-polymers5071
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.460, 47.825, 63.067
Angle α, β, γ (deg.)90.000, 98.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Focal adhesion kinase 1 / FADK 1 / pp125FAK / Protein-tyrosine kinase 2


Mass: 31757.664 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTK2, FAK, FAK1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-YAM / N-methyl-N-{3-[({2-[(2-oxo-2,3-dihydro-1H-indol-5-yl)amino]-5-(trifluoromethyl)pyrimidin-4-yl}amino)methyl]pyridin-2-yl}methanesulfonamide


Mass: 507.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20F3N7O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 15% PEG 8000, 0.1M HEPES, 0.2M (NH4)2SO4, pH 7.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 12589 / % possible obs: 91 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.073 / Χ2: 1.153 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.2820.2088161.06559.1
2.28-2.372.30.20210281.08475.9
2.37-2.482.60.19111801.07886.8
2.48-2.6130.17713051.16795.1
2.61-2.773.40.14313591.12797.5
2.77-2.993.70.12713451.18997.5
2.99-3.293.70.08913641.22399
3.29-3.763.70.06113691.24398.9
3.76-4.743.70.04413941.19599.6
4.74-503.60.03714291.01299.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.904 / SU B: 6.118 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 682 5.4 %RANDOM
Rwork0.156 ---
obs0.16 12569 91.17 %-
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: 29.821 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å21.67 Å2
2---0.7 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 35 281 2411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222179
X-RAY DIFFRACTIONr_bond_other_d00.021519
X-RAY DIFFRACTIONr_angle_refined_deg0.7941.9852949
X-RAY DIFFRACTIONr_angle_other_deg0.6283.0013679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8715256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86923.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6581518
X-RAY DIFFRACTIONr_chiral_restr0.0510.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022370
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02454
X-RAY DIFFRACTIONr_nbd_refined0.2190.2521
X-RAY DIFFRACTIONr_nbd_other0.2240.21704
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21081
X-RAY DIFFRACTIONr_nbtor_other0.0890.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.222
X-RAY DIFFRACTIONr_mcbond_it1.2051.51684
X-RAY DIFFRACTIONr_mcbond_other0.1861.5518
X-RAY DIFFRACTIONr_mcangle_it1.38722092
X-RAY DIFFRACTIONr_scbond_it2.29831058
X-RAY DIFFRACTIONr_scangle_it3.494.5857
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 29 -
Rwork0.173 553 -
all-582 -
obs--57.23 %

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