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- PDB-4qps: Crystal structure of Jak3 complexed to N-[3-(6-Phenylamino-pyrazi... -

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Basic information

Entry
Database: PDB / ID: 4qps
TitleCrystal structure of Jak3 complexed to N-[3-(6-Phenylamino-pyrazin-2-yl)-3H-benzoimidazol-5-yl]-acrylamide
ComponentsTyrosine-protein kinase JAK3
KeywordsTransferase/transferase inhibitor / Kinase catalytic domain / TRANSFERASE / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling ...negative regulation of dendritic cell cytokine production / negative regulation of FasL production / response to interleukin-9 / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / negative regulation of T-helper 1 cell differentiation / negative regulation of T cell activation / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / interleukin-4-mediated signaling pathway / interleukin-2-mediated signaling pathway / regulation of T cell apoptotic process / negative regulation of interleukin-12 production / interleukin-15-mediated signaling pathway / tyrosine phosphorylation of STAT protein / negative regulation of thymocyte apoptotic process / Interleukin-15 signaling / Interleukin-2 signaling / regulation of receptor signaling pathway via JAK-STAT / growth hormone receptor binding / Signaling by ALK / extrinsic component of plasma membrane / Interleukin-20 family signaling / negative regulation of interleukin-10 production / enzyme-linked receptor protein signaling pathway / T cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Interleukin receptor SHC signaling / extrinsic component of cytoplasmic side of plasma membrane / Interleukin-7 signaling / B cell differentiation / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / RAF/MAP kinase cascade / regulation of apoptotic process / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / cell differentiation / cytoskeleton / intracellular signal transduction / endosome / protein phosphorylation / innate immune response / ATP binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase, non-receptor Jak3 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM domain / FERM domain profile. ...Tyrosine-protein kinase, non-receptor Jak3 / Tyrosine-protein kinase, non-receptor Jak/Tyk2 / JAK, FERM F2 lobe domain / FERM F1 lobe ubiquitin-like domain / JAK1-3/TYK2, pleckstrin homology-like domain / Jak1 pleckstrin homology-like domain / FERM F2 acyl-CoA binding protein-like domain / FERM F1 ubiquitin-like domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / 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. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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-37Q / Tyrosine-protein kinase JAK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArgiriadi, M.A. / Goedken, E.R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Tricyclic Covalent Inhibitors Selectively Target Jak3 through an Active Site Thiol.
Authors: Goedken, E.R. / Argiriadi, M.A. / Banach, D.L. / Fiamengo, B.A. / Foley, S.E. / Frank, K.E. / George, J.S. / Harris, C.M. / Hobson, A.D. / Ihle, D.C. / Marcotte, D. / Merta, P.J. / Michalak, ...Authors: Goedken, E.R. / Argiriadi, M.A. / Banach, D.L. / Fiamengo, B.A. / Foley, S.E. / Frank, K.E. / George, J.S. / Harris, C.M. / Hobson, A.D. / Ihle, D.C. / Marcotte, D. / Merta, P.J. / Michalak, M.E. / Murdock, S.E. / Tomlinson, M.J. / Voss, J.W.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase JAK3
C: Tyrosine-protein kinase JAK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3174
Polymers66,6042
Non-polymers7132
Water3,585199
1
A: Tyrosine-protein kinase JAK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6592
Polymers33,3021
Non-polymers3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Tyrosine-protein kinase JAK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6592
Polymers33,3021
Non-polymers3561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.511, 43.877, 81.695
Angle α, β, γ (deg.)90.00, 115.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase JAK3 / Janus kinase 3 / JAK-3 / Leukocyte janus kinase / L-JAK


Mass: 33302.148 Da / Num. of mol.: 2 / Fragment: Jak3, unp residues 811-1103 / Mutation: C1040S, C1048S, D949A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAK3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P52333, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-37Q / N-{1-[6-(phenylamino)pyrazin-2-yl]-1H-benzimidazol-6-yl}prop-2-enamide


Mass: 356.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 1.93 Å3/Da / Density % sol: 36.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG-3350, 0.2 M ammonium sulfate and 0.1 M BisTRIS pH 5.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 23, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 47056 / Num. obs: 47056 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.36 Å2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5 / Num. unique all: 4607

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
BUSTER2.9.7refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.67 Å / Cor.coef. Fo:Fc: 0.9349 / Cor.coef. Fo:Fc free: 0.9063 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 2382 5.07 %RANDOM
Rwork0.2074 ---
obs0.2097 47010 98.52 %-
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.2182 Å20 Å2-1.2839 Å2
2---7.8615 Å20 Å2
3----0.3568 Å2
Refine analyzeLuzzati coordinate error obs: 0.223 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4352 0 54 199 4605
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014586HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046209HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1578SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes689HARMONIC5
X-RAY DIFFRACTIONt_it4586HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion17.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion549SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5613SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2517 154 4.56 %
Rwork0.2316 3221 -
all0.2325 3375 -
obs--98.52 %

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