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- PDB-5ztn: The crystal structure of human DYRK2 in complex with Curcumin -

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Basic information

Entry
Database: PDB / ID: 5ztn
TitleThe crystal structure of human DYRK2 in complex with Curcumin
ComponentsDual specificity tyrosine-phosphorylation-regulated kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor of kinase / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dual-specificity kinase / negative regulation of calcineurin-NFAT signaling cascade / smoothened signaling pathway / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / positive regulation of glycogen biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / 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 / ribonucleoprotein complex / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...DYRK / Dual specificity tyrosine-phosphorylation-regulated kinase / Trypsin Inhibitor V; Chain A / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CUR / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsJi, C.G. / Xiao, J.Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Ancient drug curcumin impedes 26S proteasome activity by direct inhibition of dual-specificity tyrosine-regulated kinase 2.
Authors: Banerjee, S. / Ji, C. / Mayfield, J.E. / Goel, A. / Xiao, J. / Dixon, J.E. / Guo, X.
History
DepositionMay 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,7794
Polymers99,0422
Non-polymers7372
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint5 kcal/mol
Surface area37440 Å2
Unit cell
Length a, b, c (Å)83.659, 83.659, 149.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

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


Mass: 49520.926 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) / Strain (production host): BL21(DE3) / References: UniProt: Q92630, dual-specificity kinase
#2: Chemical ChemComp-CUR / (1Z,4Z,6E)-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one / Curcumin, enol form


Mass: 368.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H20O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium citrate tribasic, 12%-20% PEG 3350,pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.496→40.275 Å / Num. obs: 35490 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rpim(I) all: 0.052 / Net I/σ(I): 21.8
Reflection shellResolution: 2.496→2.5 Å / Rpim(I) all: 0.632

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
PHASERphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2L

3k2l


Resolution: 2.496→40.275 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.87
RfactorNum. reflection% reflection
Rfree0.2444 1990 5.61 %
Rwork0.197 --
obs0.1997 35490 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.496→40.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 0 54 36 6522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096640
X-RAY DIFFRACTIONf_angle_d1.2468942
X-RAY DIFFRACTIONf_dihedral_angle_d12.8483986
X-RAY DIFFRACTIONf_chiral_restr0.057922
X-RAY DIFFRACTIONf_plane_restr0.0071158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4958-2.55820.37411410.30192361X-RAY DIFFRACTION99
2.5582-2.62730.31531460.28012424X-RAY DIFFRACTION100
2.6273-2.70460.35131350.27012377X-RAY DIFFRACTION100
2.7046-2.79190.33491450.25272400X-RAY DIFFRACTION100
2.7919-2.89170.30961410.25242389X-RAY DIFFRACTION100
2.8917-3.00740.36111420.25882380X-RAY DIFFRACTION100
3.0074-3.14420.36291400.26682380X-RAY DIFFRACTION100
3.1442-3.30990.30281430.23142392X-RAY DIFFRACTION100
3.3099-3.51720.25721460.21332398X-RAY DIFFRACTION100
3.5172-3.78860.23841420.20382416X-RAY DIFFRACTION100
3.7886-4.16950.20781470.17612378X-RAY DIFFRACTION100
4.1695-4.7720.18841410.14912404X-RAY DIFFRACTION100
4.772-6.0090.20161370.16932425X-RAY DIFFRACTION100
6.009-40.28030.19621440.15792376X-RAY DIFFRACTION97

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