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- PDB-7o7i: Crystal structure of the human HIPK3 kinase domain -

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Basic information

Entry
Database: PDB / ID: 7o7i
TitleCrystal structure of the human HIPK3 kinase domain
ComponentsHomeodomain-interacting protein kinase 3
KeywordsTRANSFERASE / serine/threonine kinase / CMGC kinase / transcription / homeodomain-interacting protein kinase
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
Homeodomain-interacting protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Jan 31, 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)46,2072
Polymers46,1451
Non-polymers621
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint1 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.279, 80.279, 181.989
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 69.27 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes (pH 7.5), 0.2 M MgCl2, and 15-17% (v/w) medium weight PEG mix

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 2.5→45.71 Å / Num. obs: 17854 / % possible obs: 73.69 % / Redundancy: 17 % / CC1/2: 0.89 / Rrim(I) all: 0.126 / Net I/σ(I): 12.38
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 236 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6p5s

6p5s


Resolution: 2.5→45.71 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 1789 10.02 %
Rwork0.2432 --
obs0.2464 17854 73.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 4 51 2988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013000
X-RAY DIFFRACTIONf_angle_d0.4044060
X-RAY DIFFRACTIONf_dihedral_angle_d11.4161106
X-RAY DIFFRACTIONf_chiral_restr0.037458
X-RAY DIFFRACTIONf_plane_restr0.003514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.6327160.5316154X-RAY DIFFRACTION9
2.57-2.640.6707250.6041228X-RAY DIFFRACTION14
2.64-2.730.6681420.4935395X-RAY DIFFRACTION24
2.73-2.830.4576770.4457657X-RAY DIFFRACTION40
2.83-2.940.38131300.39641122X-RAY DIFFRACTION68
2.94-3.070.36881810.34961612X-RAY DIFFRACTION96
3.07-3.240.32571780.33191665X-RAY DIFFRACTION100
3.24-3.440.39831820.29381642X-RAY DIFFRACTION100
3.44-3.70.31451860.29161675X-RAY DIFFRACTION100
3.7-4.080.27531890.24161692X-RAY DIFFRACTION100
4.08-4.670.22931880.20871696X-RAY DIFFRACTION100
4.67-5.870.24971930.22591716X-RAY DIFFRACTION100
5.88-45.710.23622020.19221811X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -43.144 Å / Origin y: 13.399 Å / Origin z: -37.777 Å
111213212223313233
T0.752 Å20.2902 Å20.1073 Å2-0.1755 Å20.0202 Å2--0.3692 Å2
L2.2822 °2-0.3673 °2-0.3262 °2-2.19 °20.7745 °2--3.3313 °2
S-0.0808 Å °0.0942 Å °0.1894 Å °-0.0405 Å °-0.0475 Å °0.0338 Å °-0.2125 Å °-0.0435 Å °0.0709 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 184:550 OR RESID 601:601 OR RESID 701:751 ) )A184 - 550
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 184:550 OR RESID 601:601 OR RESID 701:751 ) )A601
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 184:550 OR RESID 601:601 OR RESID 701:751 ) )A701 - 751

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