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- PDB-6p5s: HIPK2 kinase domain bound to CX-4945 -

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Basic information

Entry
Database: PDB / ID: 6p5s
TitleHIPK2 kinase domain bound to CX-4945
ComponentsHomeodomain-interacting protein kinase 2
Keywordstransferase/transferase inhibitor / Homeodomain Interacting Protein / Kinase / p53 regulator / Mitophagy / Fibrosis / NUCLEAR PROTEIN / transferase-transferase inhibitor complex
Function / homology
Function and homology information


lens induction in camera-type eye / iris morphogenesis / embryonic retina morphogenesis in camera-type eye / embryonic camera-type eye morphogenesis / retina layer formation / Physiological factors / PML body organization / eye development / voluntary musculoskeletal movement / YAP1- and WWTR1 (TAZ)-stimulated gene expression ...lens induction in camera-type eye / iris morphogenesis / embryonic retina morphogenesis in camera-type eye / embryonic camera-type eye morphogenesis / retina layer formation / Physiological factors / PML body organization / eye development / voluntary musculoskeletal movement / YAP1- and WWTR1 (TAZ)-stimulated gene expression / respiratory system process / SMAD protein signal transduction / virion binding / adult walking behavior / anterior/posterior pattern specification / smoothened signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / lung morphogenesis / thyroid gland development / Regulation of MECP2 expression and activity / negative regulation of BMP signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage response, signal transduction by p53 class mediator / transforming growth factor beta receptor signaling pathway / intrinsic apoptotic signaling pathway / SUMOylation of transcription cofactors / erythrocyte differentiation / regulation of signal transduction by p53 class mediator / epigenetic regulation of gene expression / positive regulation of DNA-binding transcription factor activity / peptidyl-threonine phosphorylation / positive regulation of JNK cascade / PML body / neuron differentiation / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / cytoplasmic stress granule / transcription corepressor activity / positive regulation of protein binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / gene expression / neuron apoptotic process / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / transcription coactivator activity / eukaryotic translation initiation factor 2alpha kinase activity / cell population proliferation / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / nuclear body / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3NG / Homeodomain-interacting protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsAgnew, C. / Liu, L. / Jura, N.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region.
Authors: Agnew, C. / Liu, L. / Liu, S. / Xu, W. / You, L. / Yeung, W. / Kannan, N. / Jablons, D. / Jura, N.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeodomain-interacting protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3272
Polymers44,9771
Non-polymers3501
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.155, 130.155, 52.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Homeodomain-interacting protein kinase 2 / hHIPk2


Mass: 44977.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIPK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H2X6, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-3NG / 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid


Mass: 349.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H12ClN3O2 / Comment: chemotherapy, inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M KSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1111 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1111 Å / Relative weight: 1
ReflectionResolution: 2.19→56.4 Å / Num. obs: 26108 / % possible obs: 99.98 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.021 / Rrim(I) all: 0.03 / Net I/σ(I): 17.63
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 2564 / CC1/2: 0.857 / Rpim(I) all: 0.24 / Rrim(I) all: 0.35 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.194→56.359 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 1296 4.96 %
Rwork0.1977 --
obs0.1997 26106 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→56.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 25 65 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082684
X-RAY DIFFRACTIONf_angle_d0.9763655
X-RAY DIFFRACTIONf_dihedral_angle_d5.3272176
X-RAY DIFFRACTIONf_chiral_restr0.054418
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1941-2.28190.27041430.23352716X-RAY DIFFRACTION100
2.2819-2.38580.25481420.22972731X-RAY DIFFRACTION100
2.3858-2.51160.30571410.22242738X-RAY DIFFRACTION100
2.5116-2.66890.26981400.22472729X-RAY DIFFRACTION100
2.6689-2.8750.27341400.22652766X-RAY DIFFRACTION100
2.875-3.16430.26171490.22142737X-RAY DIFFRACTION100
3.1643-3.62210.27081450.20382767X-RAY DIFFRACTION100
3.6221-4.56320.22011500.17252765X-RAY DIFFRACTION100
4.5632-56.37730.20881460.19052861X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -31.3253 Å / Origin y: 30.2717 Å / Origin z: -0.062 Å
111213212223313233
T0.4002 Å20.022 Å2-0.0491 Å2-0.4202 Å2-0.1009 Å2--0.4026 Å2
L0.7231 °20.5011 °2-0.4127 °2-1.9776 °2-0.5661 °2--1.1983 °2
S0.09 Å °-0.132 Å °-0.0314 Å °-0.0434 Å °-0.2091 Å °0.1061 Å °-0.1324 Å °-0.1336 Å °0 Å °
Refinement TLS groupSelection details: all

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