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- PDB-9kqy: The co-crystal structure of DYRK2 with YK-3-18E -

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Basic information

Entry
Database: PDB / ID: 9kqy
TitleThe co-crystal structure of DYRK2 with YK-3-18E
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsCELL CYCLE / DYRK2 / YK-3-18E
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity ...dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of glycogen biosynthetic process / ubiquitin ligase complex / protein serine/threonine/tyrosine kinase activity / regulation of signal transduction by p53 class mediator / manganese ion binding / protein tyrosine kinase activity / Regulation of TP53 Activity through Phosphorylation / cytoskeleton / protein phosphorylation / ribonucleoprotein complex / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase / : / 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
: / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTong, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82304293 China
CitationJournal: To Be Published
Title: The co-crystal structure of DYRK2 with YK-3-18E
Authors: Tong, C.
History
DepositionNov 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Dual specificity tyrosine-phosphorylation-regulated kinase 2
A: Dual specificity tyrosine-phosphorylation-regulated kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3133
Polymers93,7642
Non-polymers5491
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)223.166, 71.961, 70.229
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 2


Mass: 46882.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DYRK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92630, dual-specificity kinase
#2: Chemical ChemComp-A1L6I / [6-[[4-[2-(diethylamino)-1,3-benzothiazol-6-yl]-5-fluoranyl-pyrimidin-2-yl]amino]pyridin-3-yl]-(4-propan-2-ylpiperazin-1-yl)methanone


Mass: 548.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33FN8OS / Feature type: SUBJECT OF INVESTIGATION
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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate 0.1M Sodium citrate tribasic dihydrate pH 4.5 8% w/v PEG20000 10mM ATP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→40.14 Å / Num. obs: 18137 / % possible obs: 97.9 % / Redundancy: 3.521 % / CC1/2: 0.98 / Net I/σ(I): 8.41
Reflection shellResolution: 3.2→3.39 Å / Mean I/σ(I) obs: 1.92 / Num. unique obs: 5588 / CC1/2: 0.603 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→40.14 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2763 1815 10.01 %
Rwork0.2279 --
obs0.2327 18137 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 39 0 6301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036455
X-RAY DIFFRACTIONf_angle_d0.5418701
X-RAY DIFFRACTIONf_dihedral_angle_d4.897876
X-RAY DIFFRACTIONf_chiral_restr0.042902
X-RAY DIFFRACTIONf_plane_restr0.0061125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.36041360.32971220X-RAY DIFFRACTION98
3.28-3.380.34011370.27141244X-RAY DIFFRACTION98
3.38-3.490.30651410.25521258X-RAY DIFFRACTION98
3.49-3.610.32361370.26511239X-RAY DIFFRACTION99
3.61-3.760.3231400.25061258X-RAY DIFFRACTION99
3.76-3.930.34321380.25381247X-RAY DIFFRACTION98
3.93-4.140.27241390.21761241X-RAY DIFFRACTION99
4.14-4.390.21081400.2011266X-RAY DIFFRACTION98
4.39-4.730.22861390.18271253X-RAY DIFFRACTION99
4.73-5.210.23271420.19991267X-RAY DIFFRACTION99
5.21-5.960.26971410.22281271X-RAY DIFFRACTION99
5.96-7.50.29671410.23611271X-RAY DIFFRACTION99

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