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- PDB-8yev: Dual-specificity tyrosine phosphorylation-regulated kinase 1A in ... -

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Basic information

Entry
Database: PDB / ID: 8yev
TitleDual-specificity tyrosine phosphorylation-regulated kinase 1A in complex with coumestrol
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 1A
KeywordsHYDROLASE / inhibitor / complex / kinase
Function / homology
Function and homology information


negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 ...negative regulation of heterochromatin formation / peptidyl-serine autophosphorylation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / amyloid-beta formation / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / RNA polymerase II CTD heptapeptide repeat kinase activity / peptidyl-threonine phosphorylation / protein serine/threonine/tyrosine kinase activity / tubulin binding / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / peptidyl-tyrosine phosphorylation / tau protein binding / circadian rhythm / nervous system development / peptidyl-serine phosphorylation / actin binding / protein autophosphorylation / protein tyrosine kinase activity / transcription coactivator activity / histone H3T45 kinase activity / protein kinase activity / nuclear speck / protein phosphorylation / axon / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Coumestrol / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25152331476 Å
AuthorsLee, C.C. / Hsu, K.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Identification, biological evaluation, and crystallographic analysis of coumestrol as a novel dual-specificity tyrosine-phosphorylation-regulated kinase 1A inhibitor.
Authors: Peng, C.H. / Hwang, T.L. / Hung, S.C. / Tu, H.J. / Tseng, Y.T. / Lin, T.E. / Lee, C.C. / Tseng, Y.C. / Ko, C.Y. / Yen, S.C. / Hsu, K.C. / Pan, S.L. / HuangFu, W.C.
History
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5874
Polymers84,0512
Non-polymers5362
Water7,819434
1
A: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2942
Polymers42,0251
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2942
Polymers42,0251
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.689, 132.689, 91.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 1A / Dual specificity YAK1-related kinase / HP86 / Protein kinase minibrain homolog / MNBH / hMNB


Mass: 42025.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK1A, DYRK, MNB, MNBH / Production host: Escherichia coli (E. coli)
References: UniProt: Q13627, [RNA-polymerase]-subunit kinase, dual-specificity kinase
#2: Chemical ChemComp-CUE / Coumestrol / 3,9-dihydroxy-6H-[1]benzofuro[3,2-c]chromen-6-one


Mass: 268.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 20% Jeffamine ED-200, 0.1 M Imidazole

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 43425 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 28.4162210137 Å2 / CC1/2: 0.91 / CC star: 0.98 / Net I/σ(I): 42.2
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 4321 / CC1/2: 0.91 / CC star: 0.976

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Processing

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25152331476→24.326528802 Å / SU ML: 0.270469723248 / Cross valid method: FREE R-VALUE / σ(F): 1.35614394759 / Phase error: 24.3676429776
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23851980932 2225 5.12660998595 %
Rwork0.18450364397 41176 -
obs0.187271484388 43401 99.9700557424 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.6909353426 Å2
Refinement stepCycle: LAST / Resolution: 2.25152331476→24.326528802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5627 0 40 434 6101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008273275352925806
X-RAY DIFFRACTIONf_angle_d0.9471625758497839
X-RAY DIFFRACTIONf_chiral_restr0.0546174056427824
X-RAY DIFFRACTIONf_plane_restr0.00619994829728998
X-RAY DIFFRACTIONf_dihedral_angle_d6.966346176633475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.30040.2826071785931260.2239672140152566X-RAY DIFFRACTION99.7037037037
2.3004-2.35390.2705085174121340.2211938557852563X-RAY DIFFRACTION100
2.3539-2.41270.2631346220081360.206264512382551X-RAY DIFFRACTION100
2.4127-2.47790.2942610940691460.2033725616732567X-RAY DIFFRACTION100
2.4779-2.55070.2438606295631490.198911589162571X-RAY DIFFRACTION100
2.5507-2.6330.2663620694471190.189833932722558X-RAY DIFFRACTION100
2.633-2.7270.2536598724151580.1974369486332563X-RAY DIFFRACTION100
2.727-2.8360.2559612472711440.2025087997652547X-RAY DIFFRACTION100
2.836-2.96490.266081919731120.2118443055572586X-RAY DIFFRACTION100
2.9649-3.12090.2786369426741390.2079304416252568X-RAY DIFFRACTION100
3.1209-3.31590.2705905791181510.1933997462232557X-RAY DIFFRACTION100
3.3159-3.57120.2464738666471350.1839271644492583X-RAY DIFFRACTION100
3.5712-3.92930.2268036530051430.1734072684222581X-RAY DIFFRACTION99.9633027523
3.9293-4.49470.1883110860471370.1511952614262592X-RAY DIFFRACTION100
4.4947-5.65120.2262070670881270.1635889765612606X-RAY DIFFRACTION100
5.6512-24.320.1974615471771690.171861939872617X-RAY DIFFRACTION99.8566308244

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