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- PDB-7o7j: Crystal structure of the human HIPK3 kinase domain bound to abema... -

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Basic information

Entry
Database: PDB / ID: 7o7j
TitleCrystal structure of the human HIPK3 kinase domain bound to abemaciclib
ComponentsHomeodomain-interacting protein kinase 3
KeywordsTRANSFERASE / serine/threonine kinase / CMGC kinase / homeodomain-interacting protein kinase 3 / transcription / abemaciclib
Function / homology
Function and homology information


negative regulation of JUN kinase activity / mRNA transcription / peptidyl-threonine phosphorylation / PML body / peptidyl-serine phosphorylation / protein tyrosine kinase activity / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation ...negative regulation of JUN kinase activity / mRNA transcription / peptidyl-threonine phosphorylation / PML body / peptidyl-serine phosphorylation / protein tyrosine kinase activity / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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-6ZV / Homeodomain-interacting protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsKaltheuner, I.H. / Anand, K. / Geyer, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GE 976/9-2 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Abemaciclib is a potent inhibitor of DYRK1A and HIP kinases involved in transcriptional regulation.
Authors: Kaltheuner, I.H. / Anand, K. / Moecking, J. / Duster, R. / Wang, J. / Gray, N.S. / Geyer, M.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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 / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeodomain-interacting protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6512
Polymers46,1451
Non-polymers5071
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.064, 81.064, 178.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Homeodomain-interacting protein kinase 3 / Androgen receptor-interacting nuclear protein kinase / ANPK / Fas-interacting serine/threonine- ...Androgen receptor-interacting nuclear protein kinase / ANPK / Fas-interacting serine/threonine-protein kinase / FIST / Homolog of protein kinase YAK1


Mass: 46144.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIPK3, DYRK6, FIST3, PKY
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q9H422, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6ZV / N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine / Abemaciclib


Mass: 506.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H32F2N8 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4 Å3/Da / Density % sol: 69.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris/HCl (pH 8.0), 0.2 M MgCl2, and 8% PEG 8000 solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.81→45.44 Å / Num. obs: 17239 / % possible obs: 99.91 % / Redundancy: 16.3 % / CC1/2: 0.999 / Rrim(I) all: 0.06367 / Net I/σ(I): 23.68
Reflection shellResolution: 2.81→2.91 Å / Num. unique obs: 1679 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HIPK3

Resolution: 2.81→45.44 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2733 863 5.01 %
Rwork0.2459 16376 -
obs0.2473 17239 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.98 Å2 / Biso mean: 116.1661 Å2 / Biso min: 68.43 Å2
Refinement stepCycle: final / Resolution: 2.81→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 37 15 2995
Biso mean--98.03 113.47 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.81-2.980.35651400.332226522792
2.98-3.210.39951410.38226792820
3.21-3.540.35811430.313427002843
3.54-4.050.29411430.295127212864
4.05-5.10.26481450.239927372882
5.1-45.440.2421510.20528873038
Refinement TLS params.Method: refined / Origin x: -44.0233 Å / Origin y: 13.8086 Å / Origin z: -37.6159 Å
111213212223313233
T0.8967 Å20.1426 Å2-0.004 Å2-0.5862 Å20.0526 Å2--0.815 Å2
L3.3592 °20.0101 °20.9442 °2-1.7918 °20.4464 °2--4.9949 °2
S-0.1632 Å °-0.1196 Å °0.249 Å °0.1447 Å °-0.0608 Å °0.062 Å °-0.2903 Å °-0.1551 Å °0.2688 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA184 - 551
2X-RAY DIFFRACTION1allA900
3X-RAY DIFFRACTION1allB1 - 96

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