PDB-6z83: CK2 alpha bound to chemical probe SGC-CK2-1

ID or keywords:

Entry

Database: PDB / ID: 6z83

Title

CK2 alpha bound to chemical probe SGC-CK2-1

Components

Casein kinase II subunit alpha

Keywords

TRANSFERASE / Kinase / Chemical Probe / Inhibitor / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / Receptor Mediated Mitophagy / Synthesis of PC / Sin3-type complex / Maturation of hRSV A proteins ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.171 Å

Authors

Kraemer, A. / Wells, C. / Drewry, D.H. / Pickett, J.E. / Axtman, A.D. / Knapp, S. / Structural Genomics Consortium (SGC)

Citation

Journal: Cell Chem Biol / Year: 2021
Title: Development of a potent and selective chemical probe for the pleiotropic kinase CK2.
Authors: Wells, C.I. / Drewry, D.H. / Pickett, J.E. / Tjaden, A. / Kramer, A. / Muller, S. / Gyenis, L. / Menyhart, D. / Litchfield, D.W. / Knapp, S. / Axtman, A.D.

History

Deposition	Jun 2, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 29, 2020	Provider: repository / Type: Initial release
Revision 1.1	Feb 10, 2021	Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 28, 2021	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6z83.cif.gz	163.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6z83.ent.gz		Display	PDB format
PDBx/mmJSON format	6z83.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6z83_validation.pdf.gz	1016.4 KB	Display	wwPDB validaton report
Full document	6z83_full_validation.pdf.gz	1019.7 KB	Display
Data in XML	6z83_validation.xml.gz	28.1 KB	Display
Data in CIF	6z83_validation.cif.gz	40.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z8/6z83 ftp://data.pdbj.org/pub/pdb/validation_reports/z8/6z83	HTTPS FTP

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Related structure data

Related structure data	6z84C 6yulS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hme-2 6qy7-2 6l1z-d 5n1v-2 5h8b-2 3u87-1 6hor-d 3q9y-d 3fwq-1 5cu4-d 5oti-d 3q9x-2 4uba-2 5zn0-d 7a49-1 3u9c-1 5cqw-2 3u4u-d 6gmd-1 5zn3-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6z84C

6yulS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#141 - Sep 2011 O-GlcNAc Transferase similarity (7) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #54 - Jun 2004 Acetylcholinesterase similarity (1) #122 - Feb 2010 Enhanceosome similarity (1)

Deposited unit

AAA: Casein kinase II subunit alpha

BBB: Casein kinase II subunit alpha

hetero molecules

88.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Casein kinase II subunit alpha

hetero molecules

defined by author
Evidence: gel filtration
43.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Casein kinase II subunit alpha

hetero molecules

defined by author
44.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.960, 126.960, 124.600
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Casein kinase II subunit alpha / CK II alpha Mass: 42799.633 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK2A1, CK2A1 / Production host: Escherichia coli (E. coli) References: UniProt: P68400, non-specific serine/threonine protein kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-QBE / ~{N}-[5-[[3-cyano-7-(cyclopropylamino)-3~{H}-pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide Mass: 375.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₁N₇O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.06 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 15, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 2.17→44.89 Å / Num. obs: 54337 / % possible obs: 100 % / Redundancy: 26.5 % / CC_1/2: 0.999 / Net I/σ(I): 16.3
Reflection shell	Resolution: 2.17→2.23 Å / Num. unique obs: 4362 / CC_1/2: 0.761

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6yul

6yul

Resolution: 2.171→44.89 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.932 / SU B: 6.166 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / ESU R: 0.217 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2446	2767	5.099 %
R_work	0.214	51498	-
all	0.216	-	-
obs	-	54265	99.956 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 36.336 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.648 Å²	-0 Å²	-0 Å²
2-	-	1.648 Å²	-0 Å²
3-	-	-	-3.296 Å²

Refinement step

Cycle: LAST / Resolution: 2.171→44.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5441	0	165	275	5881

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	5741
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	5154
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.044	0.01	8386
X-RAY DIFFRACTION	r_angle_refined_deg	1.42	1.644	7771
X-RAY DIFFRACTION	r_angle_other_deg	1.495	1.59	11895
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.276	5	654
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.756	21.652	333
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.056	15	936
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.312	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	691
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6529
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1286
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1138
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	4927
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	2754
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	2643
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.12	0.2	245
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.143	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.2	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	1.475	3.825	2625
X-RAY DIFFRACTION	r_mcbond_other	1.476	3.823	2624
X-RAY DIFFRACTION	r_mcangle_it	2.452	5.725	3278
X-RAY DIFFRACTION	r_mcangle_other	2.452	5.727	3277
X-RAY DIFFRACTION	r_scbond_it	1.593	4.081	3116
X-RAY DIFFRACTION	r_scbond_other	1.593	4.081	3117
X-RAY DIFFRACTION	r_scangle_it	2.69	6.041	4487
X-RAY DIFFRACTION	r_scangle_other	2.689	6.042	4488
X-RAY DIFFRACTION	r_lrange_it	5.088	75.988	12045
X-RAY DIFFRACTION	r_lrange_other	5.088	75.988	12046

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.171-2.227	0.277	192	0.277	3748	X-RAY DIFFRACTION	99.7468
2.227-2.288	0.328	158	0.281	3659	X-RAY DIFFRACTION	99.9738
2.288-2.354	0.307	159	0.268	3610	X-RAY DIFFRACTION	99.9735
2.354-2.427	0.282	177	0.252	3459	X-RAY DIFFRACTION	99.9725
2.427-2.506	0.284	180	0.255	3367	X-RAY DIFFRACTION	100
2.506-2.594	0.302	168	0.244	3256	X-RAY DIFFRACTION	99.9708
2.594-2.692	0.266	169	0.233	3142	X-RAY DIFFRACTION	100
2.692-2.802	0.273	196	0.222	3001	X-RAY DIFFRACTION	100
2.802-2.926	0.261	193	0.213	2873	X-RAY DIFFRACTION	99.9674
2.926-3.069	0.275	158	0.214	2775	X-RAY DIFFRACTION	100
3.069-3.235	0.256	114	0.216	2687	X-RAY DIFFRACTION	100
3.235-3.431	0.245	148	0.207	2511	X-RAY DIFFRACTION	100
3.431-3.667	0.225	137	0.197	2367	X-RAY DIFFRACTION	100
3.667-3.96	0.228	111	0.184	2227	X-RAY DIFFRACTION	100
3.96-4.338	0.169	126	0.169	2048	X-RAY DIFFRACTION	100
4.338-4.848	0.16	95	0.159	1875	X-RAY DIFFRACTION	100
4.848-5.595	0.217	110	0.188	1648	X-RAY DIFFRACTION	100
5.595-6.846	0.322	83	0.231	1424	X-RAY DIFFRACTION	100
6.846-9.654	0.281	57	0.207	1143	X-RAY DIFFRACTION	100

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