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- PDB-7ejv: The co-crystal structure of DYRK2 with YK-2-69 -

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Basic information

Entry
Database: PDB / ID: 7ejv
TitleThe co-crystal structure of DYRK2 with YK-2-69
Components(Dual specificity tyrosine-phosphorylation-regulated kinase 2) x 2
KeywordsTRANSFERASE / Phosphorylase Kinase
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 / ubiquitin ligase complex / positive regulation of glycogen biosynthetic process / 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 / ubiquitin ligase complex / positive regulation of glycogen biosynthetic process / 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 / cytoplasm / cytosol
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
Chem-YK2 / Dual specificity tyrosine-phosphorylation-regulated kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLi, Z. / Xiao, Y. / Yuan, K. / Kuang, W. / Xiuquan, Y. / Yang, P.
CitationJournal: Nat Commun / Year: 2022
Title: Targeting dual-specificity tyrosine phosphorylation-regulated kinase 2 with a highly selective inhibitor for the treatment of prostate cancer.
Authors: Yuan, K. / Li, Z. / Kuang, W. / Wang, X. / Ji, M. / Chen, W. / Ding, J. / Li, J. / Min, W. / Sun, C. / Ye, X. / Lu, M. / Wang, L. / Ge, H. / Jiang, Y. / Hao, H. / Xiao, Y. / Yang, P.
History
DepositionApr 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)90,8434
Polymers89,8302
Non-polymers1,0132
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.860, 129.387, 291.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 80 through 87 or (resid 88...
21(chain B and (resid 80 through 215 or resid 217...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROMETMET(chain A and (resid 80 through 87 or (resid 88...AA80 - 873 - 10
12LYSLYSLYSLYS(chain A and (resid 80 through 87 or (resid 88...AA8811
13ALAALAARGARG(chain A and (resid 80 through 87 or (resid 88...AA78 - 4641 - 387
14ALAALAARGARG(chain A and (resid 80 through 87 or (resid 88...AA78 - 4641 - 387
15ALAALAARGARG(chain A and (resid 80 through 87 or (resid 88...AA78 - 4641 - 387
16ALAALAARGARG(chain A and (resid 80 through 87 or (resid 88...AA78 - 4641 - 387
21PROPROLEULEU(chain B and (resid 80 through 215 or resid 217...BB80 - 2151 - 136
22ASNASNLYSLYS(chain B and (resid 80 through 215 or resid 217...BB217 - 371138 - 292
23LEULEUTHRTHR(chain B and (resid 80 through 215 or resid 217...BB373 - 396294 - 317
24ASPASPLEULEU(chain B and (resid 80 through 215 or resid 217...BB399 - 443320 - 364
25TRPTRPARGARG(chain B and (resid 80 through 215 or resid 217...BB445 - 464366 - 385

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Components

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


Mass: 44655.473 Da / Num. of mol.: 1
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: Protein Dual specificity tyrosine-phosphorylation-regulated kinase 2


Mass: 45174.160 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-YK2 / [6-[[4-[2-(dimethylamino)-1,3-benzothiazol-6-yl]-5-fluoranyl-pyrimidin-2-yl]amino]pyridin-3-yl]-(4-ethylpiperazin-1-yl)methanone


Mass: 506.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27FN8OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 8% PEG3350

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→19.86 Å / Num. obs: 40357 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Net I/σ(I): 14.02
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 3967 / CC1/2: 0.696 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
XDSdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXD

5lxd


Resolution: 2.5→19.86 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2477 3.22 %
Rwork0.2007 74359 -
obs0.2021 40357 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.3 Å2 / Biso mean: 72.87 Å2 / Biso min: 29.94 Å2
Refinement stepCycle: final / Resolution: 2.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 72 35 6368
Biso mean--65.81 55.22 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016519
X-RAY DIFFRACTIONf_angle_d1.3028801
X-RAY DIFFRACTIONf_chiral_restr0.069909
X-RAY DIFFRACTIONf_plane_restr0.0091135
X-RAY DIFFRACTIONf_dihedral_angle_d10.0435506
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3571X-RAY DIFFRACTION13TORSIONAL
12B3571X-RAY DIFFRACTION13TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.5480.39221380.36364210
2.5999-2.65630.3571390.29994194
2.6563-2.71790.29281360.29164049
2.7179-2.78570.3371400.28024164
2.7857-2.86080.31061370.28294154
2.8608-2.94480.35411410.26314115
2.9448-3.03950.27091390.25194104
3.0395-3.14770.30311370.24364105
3.1477-3.27320.30961410.22634170
3.2732-3.42150.21551390.20014139
3.4215-3.60090.24781420.18664139
3.6009-3.8250.21011330.1824113
3.825-4.1180.25141390.17624134
4.118-4.5280.21511360.1574122
4.528-5.17320.19431400.15544146
5.1732-6.48030.2611350.19144136
Refinement TLS params.Method: refined / Origin x: -10.54 Å / Origin y: -11.1025 Å / Origin z: 41.7861 Å
111213212223313233
T0.3904 Å20.0213 Å20.0137 Å2-0.3908 Å20.1018 Å2--0.4626 Å2
L0.6919 °2-0.0628 °2-0.2115 °2-2.5322 °20.5169 °2--0.6782 °2
S0.0289 Å °0.0802 Å °0.1786 Å °-0.5714 Å °-0.0073 Å °0.069 Å °-0.1364 Å °0.0024 Å °-0.0041 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 464
2X-RAY DIFFRACTION1allB80 - 470
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 42

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