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- PDB-8rdk: Crystal structure of human Haspin (GSG2) kinase bound to MD420 -

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Basic information

Entry
Database: PDB / ID: 8rdk
TitleCrystal structure of human Haspin (GSG2) kinase bound to MD420
ComponentsSerine/threonine-protein kinase haspin
KeywordsTRANSFERASE / Haspin / Kinase / Inhibitor
Function / homology
Function and homology information


histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity ...histone H3T3 kinase activity / protein localization to chromosome, centromeric region / mitotic sister chromatid cohesion / mitotic spindle assembly checkpoint signaling / spindle / mitotic cell cycle / chromosome / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein serine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase haspin, C-terminal / Haspin like kinase domain / Domain of unknown function / 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
: / Serine/threonine-protein kinase haspin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKraemer, A. / Defois, M. / Giraud, F. / Moreau, P. / Anizon, F. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
Citation
Journal: Eur.J.Med.Chem. / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting.
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
#1: Journal: Biorxiv / Year: 2024
Title: Synthesis and evaluation of chemical linchpins for highly selective CK2 alpha targeting
Authors: Greco, F.A. / Kramer, A. / Wahl, L. / Elson, L. / Ehret, T.A.L. / Gerninghaus, J. / Mockel, J. / Muller, S. / Hanke, T. / Knapp, S.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Revision 1.2Aug 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase haspin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1404
Polymers40,7111
Non-polymers4293
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.509, 78.199, 86.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine/threonine-protein kinase haspin / Germ cell-specific gene 2 protein / H-haspin / Haploid germ cell-specific nuclear protein kinase


Mass: 40711.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HASPIN, GSG2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TF76, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-YQT / 3-pyridin-4-yl-1~{H}-pyrrolo[3,2-g]isoquinoline


Mass: 245.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 51% MPD 0.1M SPG 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2→86.87 Å / Num. obs: 32717 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 2387 / CC1/2: 0.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→52.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.726 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23294 1599 4.9 %RANDOM
Rwork0.19695 ---
obs0.19868 31054 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.312 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å2-0 Å2
2---0.26 Å20 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 2→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 28 133 2780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162560
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6513664
X-RAY DIFFRACTIONr_angle_other_deg0.5031.5895910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.263512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27710484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9862.5051311
X-RAY DIFFRACTIONr_mcbond_other1.9812.5041311
X-RAY DIFFRACTIONr_mcangle_it2.6974.4841637
X-RAY DIFFRACTIONr_mcangle_other2.7024.4851638
X-RAY DIFFRACTIONr_scbond_it3.5132.8991398
X-RAY DIFFRACTIONr_scbond_other3.5112.9041399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1595.1762028
X-RAY DIFFRACTIONr_long_range_B_refined6.95925.863044
X-RAY DIFFRACTIONr_long_range_B_other6.97725.873045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 116 -
Rwork0.28 2264 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -9.9671 Å / Origin y: -5.9861 Å / Origin z: 7.9796 Å
111213212223313233
T0.2184 Å2-0.0215 Å20.0001 Å2-0.0264 Å2-0.0136 Å2--0.0122 Å2
L0.7364 °2-0.3265 °20.4083 °2-1.7488 °2-0.7005 °2--1.4404 °2
S-0.0317 Å °0.0776 Å °-0.0709 Å °-0.1261 Å °0.0594 Å °0.0585 Å °0.0874 Å °-0.0348 Å °-0.0277 Å °

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