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- PDB-4e93: Crystal structure of human Feline Sarcoma Viral Oncogene Homologu... -

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Basic information

Entry
Database: PDB / ID: 4.0E+93
TitleCrystal structure of human Feline Sarcoma Viral Oncogene Homologue (v-FES)in complex with TAE684
ComponentsTyrosine-protein kinase Fes/Fps
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / V-FES / FUJINAMI / AVIAN SARCOMA / VIRAL / ONCOGENE / FELINE SARCOMA VIRUS / ATP-BINDING / KINASE / NUCLEOTIDE-BINDING / PHOSPHOPROTEIN / PROTO-ONCOGENE / SH2 DOMAIN / TRANSFERASE / TYROSINE-PROTEIN KINASE / TRANSFERASE-TRANSFERASE INHIBITOR complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / regulation of cell differentiation / immunoglobulin receptor binding / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cytoplasmic side of plasma membrane / chemotaxis / microtubule cytoskeleton / regulation of cell shape / regulation of cell population proliferation / cytoplasmic vesicle / protein tyrosine kinase activity / microtubule binding / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-GUI / Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsFilippakopoulos, P. / Salah, E. / Miduturu, C.V. / Fedorov, O. / Cooper, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Gray, N.S. ...Filippakopoulos, P. / Salah, E. / Miduturu, C.V. / Fedorov, O. / Cooper, C. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Gray, N.S. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Chem.Biol. / Year: 2012
Title: Small-Molecule Inhibitors of the c-Fes Protein-Tyrosine Kinase.
Authors: Hellwig, S. / Miduturu, C.V. / Kanda, S. / Zhang, J. / Filippakopoulos, P. / Salah, E. / Deng, X. / Choi, H.G. / Zhou, W. / Hur, W. / Knapp, S. / Gray, N.S. / Smithgall, T.E.
History
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase Fes/Fps
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3722
Polymers42,7581
Non-polymers6141
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 35.330, 100.720
Angle α, β, γ (deg.)90.000, 96.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase Fes/Fps / Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c- ...Feline sarcoma/Fujinami avian sarcoma oncogene homolog / Proto-oncogene c-Fes / Proto-oncogene c-Fps / p93c-fes


Mass: 42758.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FES, FPS / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P07332, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-GUI / 5-CHLORO-N-[2-METHOXY-4-[4-(4-METHYLPIPERAZIN-1-YL)PIPERIDIN-1-YL]PHENYL]-N'-(2-PROPAN-2-YLSULFONYLPHENYL)PYRIMIDINE-2,4-DIAMINE / 4-[1-(4-{[5-CHLORO-4-({2-[(1-METHYLETHYL)SULFONYL]PHENYL}AMINO)PYRIMIDIN-2-YL]AMINO}-3-METHOXYPHENYL)PIPERIDIN-4-YL]-1-METHYLPIPERAZIN-1-IUM


Mass: 614.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40ClN7O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M SPG, 30.0% PEG 1K, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Av σ(I) over netI: 8 / Number: 160311 / Rsym value: 0.084 / D res high: 1.84 Å / D res low: 27.969 Å / Num. obs: 33290 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.8227.9799.110.0310.0314.6
4.115.8210010.0290.0294.8
3.364.1199.910.0410.0414.9
2.913.3699.310.0650.0654.9
2.62.9199.210.0920.0924.9
2.382.698.910.1390.1394.9
2.22.389810.1970.1974.9
2.062.297.210.2870.2874.8
1.942.0696.510.4210.4214.8
1.841.9495.910.7210.7214.7
ReflectionResolution: 1.84→28.93 Å / Num. all: 33969 / Num. obs: 33290 / % possible obs: 98 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.84-1.944.70.7211.12210847010.72195.9
1.94-2.064.80.4211.82153745070.42196.5
2.06-2.24.80.2872.72053642560.28797.2
2.2-2.384.90.1973.91930239760.19798
2.38-2.64.90.1395.51808737190.13998.9
2.6-2.914.90.0928.11650133910.09299.2
2.91-3.364.90.06510.81459729840.06599.3
3.36-4.114.90.04116.51265325930.04199.9
4.11-5.824.80.02922.6972920150.029100
5.82-27.9694.60.03114.7526111480.03199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.63 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å27.97 Å
Translation3.5 Å27.97 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BKB

3bkb


Resolution: 1.84→27.969 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2209 / WRfactor Rwork: 0.1714 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8755 / SU B: 5.361 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1411 / SU Rfree: 0.1406 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1688 5.1 %RANDOM
Rwork0.1859 ---
all0.1885 33944 --
obs0.1885 33285 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 277.15 Å2 / Biso mean: 32.6003 Å2 / Biso min: 6.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.42 Å2
2--0.35 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.84→27.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 42 258 3087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022921
X-RAY DIFFRACTIONr_bond_other_d0.0010.021977
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.9793977
X-RAY DIFFRACTIONr_angle_other_deg1.0553.0024775
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.06723.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72115464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9021519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 99 -
Rwork0.362 2145 -
all-2244 -
obs--95.82 %
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)
13.6253-0.06880.06273.25750.08065.06920.09110.1601-0.1153-0.2729-0.0576-0.3782-0.00251.1684-0.03360.18580.01560.00540.4385-0.02630.146416.912413.2191-7.5667
20.1536-0.32510.27151.2811-0.17135.0780.01660.07230.0309-0.32810.0536-0.0086-0.22320.1558-0.07020.1451-0.0904-0.01640.11710.03340.10582.722214.569918.9041
31.99760.4130.53481.84780.16931.1622-0.05770.1608-0.0244-0.0470.1181-0.01870.05020.049-0.06030.0117-0.00540.00940.0171-0.00110.03159.33274.327839.7784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A447 - 550
2X-RAY DIFFRACTION2A551 - 654
3X-RAY DIFFRACTION3A655 - 822

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