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5y9m

Crystal structure of CK2a2 form 3

Method: X-RAY DIFFRACTION Dmax: 104.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;Casein kinase II subunit alpha' ;

Homo sapiens

UniProt P19784

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain X； UniProt 1–334 Fragment：UNP residues 1-334 NIO NICOTINIC ACID × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；26% PEG 4000, 0.15 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride (pH 8.5) Resolution 2.01 Å R-free 0.205
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–334 Fragment：UNP residues 1-334 NIO NICOTINIC ACID × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；281 K；26% PEG 4000, 0.15 M Lithium sulfate monohydrate, 0.1 M TRIS hydrochloride (pH 8.5) Resolution 2.01 Å R-free 0.205

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5Y9M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3E3B Crystal structure of catalytic subunit of human protein kinase CK2alpha prime with a potent indazole-derivative inhibitor Deposited 2008-08-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 1–334（334 aa） Fragment：residues in database 1-334
Not recorded CCK [1-(6-{6-[(1-methylethyl)amino]-1H-indazol-1-yl}pyrazin-2-yl)-1H-pyrrol-3-yl]acetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；8% PEG8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.20 Å R-free 0.274
3E3B Crystal structure of catalytic subunit of human protein kinase CK2alpha prime with a potent indazole-derivative inhibitor Deposited 2008-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain X 1–334（334 aa） Fragment：residues in database 1-334
Not recorded CCK [1-(6-{6-[(1-methylethyl)amino]-1H-indazol-1-yl}pyrazin-2-yl)-1H-pyrrol-3-yl]acetic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；8% PEG8000, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 3.20 Å R-free 0.274
3OFM Structure of a human CK2alpha prime, the paralog isoform of the catalytic subunit of protein kinase CK2 from Homo sapiens Deposited 2010-08-15 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S 4B0 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Protein stock solution: 6 mg/ml protein, 25 mM Tris/HCl, pH 8.5, 500 mM sodium chloride, 1 mM inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol Reservoir: 28 % PEG6000, 500 mM lithium chloride, 100 mM Tris/HCl, pH 8.5 Drop: mixture of 0.5 uL protein solution plus 0.5 uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.207
3U87 Structure of a chimeric construct of human CK2alpha and human CK2alpha' in complex with a non-hydrolysable ATP-analogue Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 327–350（24 aa） Fragment：;KINASE II SUBUNIT ALPHA (UNP RESIDUES 1-325), KINASE II SUBUNIT ALPHA' (UNP RESIDUES 327-350) ;
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；reservoir: 15% polyethylene glycol 8000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 0.8 uL reservoir solution, 0.8 uL protein solution (12.6 mg/ml), 0.5 uL 10% anapoe 305 (detergent), 1.5 uL 5 mM AMPPNP, 1.5 uL 10 mM magnesium chloride, 1.5 uL CK2 substrate peptide (sequence RRRADDSDDDDD), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.90 Å R-free 0.218
3U87 Structure of a chimeric construct of human CK2alpha and human CK2alpha' in complex with a non-hydrolysable ATP-analogue Deposited 2011-10-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 327–350（24 aa） Fragment：;KINASE II SUBUNIT ALPHA (UNP RESIDUES 1-325), KINASE II SUBUNIT ALPHA' (UNP RESIDUES 327-350) ;
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；reservoir: 15% polyethylene glycol 8000, 15% glycerol, 0.17 M ammonium sulfate, 0.1 M sodium cacodylate buffer; drop: 0.8 uL reservoir solution, 0.8 uL protein solution (12.6 mg/ml), 0.5 uL 10% anapoe 305 (detergent), 1.5 uL 5 mM AMPPNP, 1.5 uL 10 mM magnesium chloride, 1.5 uL CK2 substrate peptide (sequence RRRADDSDDDDD), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.90 Å R-free 0.218
5M4U ORTHORHOMBIC COMPLEX STRUCTURE OF HUMAN PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') WITH THE INHIBITOR 4'-CARBOXY-6,8-CHLORO- FLAVONOL (FLC21) Deposited 2016-10-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：Asp39Gly, Cys336Ser 7FC 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid × 1 GOL GLYCEROL × 5 ACT ACETATE ION × 3 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'D39G-C336S IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 25 % PEG5000 MME, 0.2 M ammonium sulphate, 0.1 M MES buffer, pH 6.5; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION
Resolution 2.19 Å R-free 0.214
5M56 Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2alpha') with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) Deposited 2016-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：D39G, C336S 7FC 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'-D39G-C336S IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 25 % PEG4000, 15 % glycerol, 0.17 M sodium acetate, 0.08 M Tris/HCl, pH 8.5; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION
Resolution 2.24 Å R-free 0.206
5M56 Monoclinic complex structure of human protein kinase CK2 catalytic subunit (isoform CK2alpha') with the inhibitor 4'-carboxy-6,8-chloro-flavonol (FLC21) Deposited 2016-10-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–350（350 aa）
Mutation：D39G, C336S 7FC 4-[6,8-bis(chloranyl)-3-oxidanyl-4-oxidanylidene-chromen-2-yl]benzoic acid × 1 GOL GLYCEROL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PROTEIN STOCK SOLUTION: 5.5 MG/ML CK2ALPHA'-D39G-C336S IN 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5; INHIBITOR STOCK SOLUTION: 10 MM INHIBITOR IN DMSO; PROTEIN/INHIBITOR COMPLEX SOLUTION: 90 MICROLITER PROTEIN STOCK SOLUTION + 10 MICROLITER INHIBITOR STOCK SOLUTION; RESERVOIR SOLUTION: 25 % PEG4000, 15 % glycerol, 0.17 M sodium acetate, 0.08 M Tris/HCl, pH 8.5; DROP SOLUTION BEFORE EQULIBRATION: 0.3 MICROLITER PROTEIN/INHIBITOR COMPLEX SOLUTION + 0.3 MICROLITER RESERVOIR SOLUTION
Resolution 2.24 Å R-free 0.206
5OOI STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P Deposited 2017-08-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S 9YE 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；90 MIKROLITER ENZYME STOCK SOLUTION (5 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/ V) PEG3350, 0.2 M AMMONIUM ACETATE, 0.1 M HEPES BUFFER, PH 8.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Resolution 2.00 Å R-free 0.221
5OOI STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA') IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR 4P Deposited 2017-08-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–350（350 aa）
Mutation：C336S 9YE 4-(3-methylbut-2-enoxy)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；90 MIKROLITER ENZYME STOCK SOLUTION (5 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 10 MIKROLITER 4P STOCK SOLUTION (10 MM 4P IN DMSO). THIS MIXTURE WAS INCUBATED FOR 30 MIN AT ROOM TEMPERATURE. THE RESERVOIR SOLUTION OF THE CRYSTALLIZATION EXPERIMENT WAS 25 % (W/ V) PEG3350, 0.2 M AMMONIUM ACETATE, 0.1 M HEPES BUFFER, PH 8.5. PRIOR TO EQUILIBRATION THE CRYSTALLIZATION DROP WAS COMPOSED OF 1 MIKROLITER RESERVOIR SOLUTION PLUS 1 MIKROLITER ENZYME/4P MIXTURE., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Resolution 2.00 Å R-free 0.221
5YF9 Crystal structure of CK2a2 form-2 Deposited 2017-09-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 1–334（334 aa） Fragment：UNP residues 1-334
Not recorded NIO NICOTINIC ACID × 1 SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；24%w/v PEG 4000, 0.15 M Lithium Sulfate mono hydrate, 0.1 M Tris-HCl (pH 8.5)
Resolution 1.89 Å R-free 0.263
5YF9 Crystal structure of CK2a2 form-2 Deposited 2017-09-20 Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–334（334 aa） Fragment：UNP residues 1-334
Not recorded NIO NICOTINIC ACID × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；24%w/v PEG 4000, 0.15 M Lithium Sulfate mono hydrate, 0.1 M Tris-HCl (pH 8.5)
Resolution 1.89 Å R-free 0.263
5YWM Crystal structure of CK2a2 form-1 Deposited 2017-11-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 1–334（334 aa）
Not recorded SO4 SULFATE ION × 2 NIO NICOTINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；PEG 4000, Lithium sulfate monohydrate
Resolution 1.94 Å R-free 0.243
6HMB STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 Gene product) IN COMPLEX WITH the inhibitor CX-4945 (Silmitasertib) Deposited 2018-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 2 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WERE MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against CX-4945 by an extensive soaking procedure of several steps.
Resolution 1.04 Å R-free 0.146
6HMC STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR THN27 Deposited 2018-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S EDO 1,2-ETHANEDIOL × 8 FXB 5-propan-2-yl-4-prop-2-enoxy-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WERE MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against THN27 by an extensive soaking procedure of several steps.
Resolution 1.03 Å R-free 0.136
6HMD STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR AR18 Deposited 2018-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S EDO 1,2-ETHANEDIOL × 2 GDW 5-[2-(diethylamino)ethyl]-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WAS MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (700 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against AR18 by an extensive soaking procedure of several steps.
Resolution 1.00 Å R-free 0.172
6HMQ STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BENZOTRIAZOLE-TYPE INHIBITOR MB002 Deposited 2018-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–346（346 aa）
Mutation：C336S TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 10 CL CHLORIDE ION × 2 NA SODIUM ION × 1 4B0 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITERs ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and Incubated WITH 20 MIKROLITERS of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF resulting solution WERE MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET on the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method.
Resolution 0.97 Å R-free 0.132
6L20 Crystal structure of CK2a2 with hematein Deposited 2019-10-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–333（333 aa）
Not recorded E3U (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 8000
Resolution 3.09 Å R-free 0.326
6L20 Crystal structure of CK2a2 with hematein Deposited 2019-10-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–333（333 aa）
Not recorded E3U (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 8000
Resolution 3.09 Å R-free 0.326
6L20 Crystal structure of CK2a2 with hematein Deposited 2019-10-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–333（333 aa）
Not recorded E3U (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 8000
Resolution 3.09 Å R-free 0.326
6L20 Crystal structure of CK2a2 with hematein Deposited 2019-10-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain J 1–333（333 aa）
Not recorded E3U (6aR)-3,4,6a,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2,1-c]chromen-9-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；PEG 8000
Resolution 3.09 Å R-free 0.326
6QY8 Human CSNK2A2 bound to ERB-041 Deposited 2019-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–335（335 aa）
Not recorded 041 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG10000, 0.1M HEPES pH 7.5
Resolution 1.70 Å R-free 0.291
6QY8 Human CSNK2A2 bound to ERB-041 Deposited 2019-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–335（335 aa）
Not recorded 041 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG10000, 0.1M HEPES pH 7.5
Resolution 1.70 Å R-free 0.291
6QY8 Human CSNK2A2 bound to ERB-041 Deposited 2019-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–335（335 aa）
Not recorded 041 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG10000, 0.1M HEPES pH 7.5
Resolution 1.70 Å R-free 0.291
6QY8 Human CSNK2A2 bound to ERB-041 Deposited 2019-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–335（335 aa）
Not recorded 041 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG10000, 0.1M HEPES pH 7.5
Resolution 1.70 Å R-free 0.291
6QY9 Human CSNK2A2 bound to a Pyrrolo[2,3-d]pyrimidinyl inhibitor Deposited 2019-03-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–335（335 aa）
Not recorded JL2 3-[3-[2-[(3,4,5-trimethoxyphenyl)amino]pyrrolo[2,3-d]pyrimidin-7-yl]phenyl]propanenitrile × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG3350, 0.2 M potassium nitrate
Resolution 1.50 Å R-free 0.165
6TE2 Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor 17 Deposited 2019-11-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded N4N 3-[(4-pyridin-2-yl-1,3-thiazol-2-yl)amino]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpja' (mutant Cys336Ser) /inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha-'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the 2-aminothiazole-type inhibitor 17 by extensive crystal soaking.
Resolution 0.92 Å R-free 0.146
6TEW Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor 27 Deposited 2019-11-12 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded N5Q 4-[(4-naphthalen-2-yl-1,3-thiazol-2-yl)amino]-2-oxidanyl-benzoic acid × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；RESERVOIR COMPOSITION: 28 % (W/V) PEG6000, 0.9 M LICL, 0.1 M, TRIS/HCL, PH 8.5; CRYSTALLIZATION DROP COMPOSITION PRIOR TO EQUILIBRATION: 0.01 ML RESERVOIR SOLUTION PLUS 0.02 ML CK2ALPHA' (MUTANT CYS336SER)/INHIBITOR MB002 MIXTURE (0.180 ML 6 MG/ML CK2ALPHA-'CYS336SER, 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5, MIXED AND PRE-EQUILIBRATED WITH 0.02 ML 10 MM MB002 IN DIMETHYL SULFOXIDE); the inhibitor MB002 was replaced by extensive soaking with the 2-aminothiazole-type inhibitor 27; VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Resolution 1.08 Å R-free 0.169
6TGU Crystal structure of human protein kinase CK2alpha'(CSNK2A2 gene product) in complex with the 2-aminothiazole-type inhibitor Cl-OH-3 Deposited 2019-11-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded N92 4-[[4-(4-chlorophenyl)-1,3-thiazol-2-yl]amino]-2-oxidanyl-benzoic acid × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；RESERVOIR COMPOSITION: 28 % (W/V) PEG6000, 0.9 M LICL, 0.1 M, TRIS/HCL, PH 8.5; CRYSTALLIZATION DROP COMPOSITION PRIOR TO EQUILIBRATION: 0.01 ML RESERVOIR SOLUTION PLUS 0.02 ML CK2ALPHA' (MUTANT CYS336SER)/INHIBITOR MB002 MIXTURE (0.180 ML 6 MG/ML CK2ALPHA-'CYS336SER, 0.5 M NACL, 25 MM TRIS/HCL, PH 8.5, MIXED AND PRE-EQUILIBRATED WITH 0.02 ML 10 MM MB002 IN DIMETHYL SULFOXIDE); THE INHIBITOR MB002 WAS REPLACED BY EXTENSIVE SOAKING WITH THE 2-AMINOTHIAZOLE-TYPE INHIBITOR Cl-OH-3
Resolution 0.83 Å R-free 0.167
7A1B Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine Deposited 2020-08-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S QXW 5,6-dibromo-1H-triazolo[4,5-b]pyridine × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Resolution 1.29 Å R-free 0.193
7A1Z Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine Deposited 2020-08-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded QWN 6-bromanyl-5-chloranyl-1~{H}-[1,2,3]triazolo[4,5-b]pyridine × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 6-bromo-5-chloro-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Resolution 1.02 Å R-free 0.147
7A22 Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine Deposited 2020-08-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 13 QWW 5,6,7-tris(bromanyl)-1~{H}-[1,2,3]triazolo[4,5-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine by extensive crystal soaking.
Resolution 1.01 Å R-free 0.166
7A2H Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-imidazo[4,5-b]pyridine Deposited 2020-08-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded QX2 5,6,7-tris(bromanyl)-1~{H}-imidazo[4,5-b]pyridine × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6,7-tribromo-1H-imidazo[4,5-b]pyridine by extensive crystal soaking.
Resolution 1.01 Å R-free 0.149
7AT9 Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the ATP-competitive inhibitor MB002 and the alphaD-pocket ligand 3,4-dichlorophenethylamine Deposited 2020-10-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded 42J 2-(3,4-dichlorophenyl)ethanamine × 2 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 7 4B0 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the alphaD-pocket ligand 3,4-dichlorophenethylamine was introduced by extensive soaking.
Resolution 1.05 Å R-free 0.150
7ATV Structure of protein kinase ck2 catalytic subunit (csnk2a2 gene product) in complex with the bivalent inhibitor KN2 Deposited 2020-10-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 RXE ~{N}'-[2-(3,4-dichlorophenyl)ethyl]-~{N}-[4-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]butyl]butanediamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser) /inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the bivalent inhibitor KN2 by extensive crystal soaking.
Resolution 0.98 Å R-free 0.141
7XYH Crystal structure of CK2a2 complexed with AG1112 Deposited 2022-06-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–334（334 aa）
Not recorded 8BH 5-azanyl-3-[(~{Z})-1-cyano-2-(1~{H}-indol-3-yl)ethenyl]-1~{H}-pyrazole-4-carbonitrile × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；PEG 10000, Tris-HCl pH 8.0, Sucrose
Resolution 2.04 Å R-free 0.282
7XYH Crystal structure of CK2a2 complexed with AG1112 Deposited 2022-06-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–334（334 aa）
Not recorded 8BH 5-azanyl-3-[(~{Z})-1-cyano-2-(1~{H}-indol-3-yl)ethenyl]-1~{H}-pyrazole-4-carbonitrile × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；PEG 10000, Tris-HCl pH 8.0, Sucrose
Resolution 2.04 Å R-free 0.282
8Q77 STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BISUBSTRATE INHIBITOR ARC-780 Deposited 2023-08-15 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded LN3 (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[12-[[4-[[5-(4-carboxyphenyl)-1,3-thiazol-2-yl]amino]-4-oxidanylidene-butanoyl]-(2-hydroxy-2-oxoethyl)amino]dodecanoylamino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]butanedioic acid × 2 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING AND PURGED TWICE WITH RESERVOIR SOLUTION. THEN, ARC-780 WAS ADDED TO AN INITIAL CONCENTRATION OF 1 MM BY ADDING 1 MIKROLITER OF A 10 MM ARC-780 SOLUTION IN DMSO IN A 1:10 RATIO TO THE DROPLET. AFTER EXTENSIVE INTIAL SOAKING, THE SALT CONCENTRATION WAS SUCCESSIVELY LOWERED OVER A PERIOD OF 8 MONTHS WHILE IN PARALLEL THE CONCENTRATIONS OF DMSO AND PEG 6000 WERE INCREASED. THIS WAS DONE BY GRADUALLY REPLACING THE RESERVOIR AND THE DROPLET SOLUTION UNTIL ANY NACL WAS REMOVED, THE LICL CONCENTRATION WAS REDUCED TO 50 MM, THE PEG 6000 CONCENTRATION WAS INCREASED TO SATURATION AND A DMSO CONTENT OF 30% WAS REACHED. MEANWHILE, THE ARC-780 LIGAND WAS INCLUDED IN ANY DESALTING STEP REACHING SATURATION AFTER THE FINAL DILUTION STEP. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.25 Å R-free 0.157
8Q9S STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR SGC-CK2-1 Deposited 2023-08-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded QBE ~{N}-[5-[[3-cyano-7-(cyclopropylamino)-3~{H}-pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]propanamide × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING SGC-CK2-1 (10 MM IN DMSO) TO A FINAL CONCENTRATION OF 2.5 MM TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002 BY SGC-CK2-1. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.35 Å R-free 0.169
8QBU STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR CX-4945 AND THE ALPHA-D-POCKET LIGAND 3,4-DICHLORO PHENETHYLAMINE (DPA) Deposited 2023-08-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 12 42J 2-(3,4-dichlorophenyl)ethanamine × 1 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. A CRYSTAL WAS PURGED TWICE WITH RESERVOIR SOLUTION BEFORE ADDING 1 MIKROLITER DPA (50 MM IN DMSO) AND 1 MIKROLITER CX-4945 (10 MM IN DMSO) TO THE CRYSTAL MOTHOR LIQUOR FOR EXTENSIVE SOAKING AND REPLACEMENT OF THE INITIAL INHIBITOR MB002. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.09 Å R-free 0.179
8QCD STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INHIBITOR 4,5,6,7-TETRABROMOBENZOTRIAZOLE Deposited 2023-08-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 TBS 4,5,6,7-TETRABROMOBENZOTRIAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN A 1:10 RATIO WITH A 20 MM SOLUTION OF 4,5,6,7-TETRABROMOBENZOTRIAZOLE (TBBT) IN DMSO. AFTER INCUBATION ON ICE FOR 30 MIN AND CENTRIFUGATION (16100 TIMES G FOR 2 MIN AT ROOM TEMPERATUR) 10 MIKROLITER OF THE SUPERNATANT WERE MIXED WITH 5 MIKORLITER OF THE RESERVOIR SOLUTION [900 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCl, PH 8.5]. AFTER EQUILIBRATION, MICROSEEDING WAS CARRIED OUT TO INDUCE CRYSTAL GROWTH. SMALL CRYSTALS APPEARED AFTER ONE WEEK. ONE OF THEM WAS USED AS A MACROSEED TRANSFERING IT TO A SECOND DROP PREPARED IN THE SAME MANNER AS THE FIRST ONE. ALL CRSTALLIZATION STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.03 Å R-free 0.156
8QCG STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE ATP ANALOGUE AMPPNP Deposited 2023-08-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE ATP-ANALOGUE AMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM AMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM AMPPNP, 60 MM MGCL2. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.04 Å R-free 0.170
8QCG STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE ATP ANALOGUE AMPPNP Deposited 2023-08-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–350（350 aa）
Mutation：C336S ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE ATP-ANALOGUE AMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM AMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM AMPPNP, 60 MM MGCL2. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.04 Å R-free 0.170
8QF1 STRUCTURE OF THE CATALYTIC SUBUNIT OF PROTEIN KINASE CK2 (CK2ALPHA') IN COMPLEX WITH THE NON-HYDROLYZABLE GTP ANALOGUE GMPPNP Deposited 2023-09-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–350（350 aa）
Chain B 1–350（350 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10 MIKROLITER CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WERE MIXED WITH 5 MIKROLITER RESERVOIR SOLUTION [810 MM LICL, 28% (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5]. AFTER EQUILIBRATION (SITTING DROP PLATES; VAPOUR DIFFUSION), CRYSTALLIZATION WAS INITIATED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING. THE GTP-ANALOGUE GMPPNP WAS COMBINED WITH THESE CRYSTALS BY SOAKING. A 20 MM GMPPNP SOLUTION IN 60 MM MGCL2 WAS PREPARED. FOR SOAKING, 3 MICROLITER OF THE CRYSTAL MOTHER LIQUOR WAS REMOVED AND REPLACED BY 3 MICROLITER OF 20 MM GMPPNP, 60 MM MGCL2. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Resolution 1.32 Å R-free 0.232
9FBI Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening Deposited 2024-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–350（350 aa）
Not recorded NIO NICOTINIC ACID × 1 EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；protein solution: 90 mikroliter CK2alpha'-Cys336Ser solution (5 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 10 mikroliter 10 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 810 mmol/l LiCl, 100 mM Tris/HCl, pH 8.5, 28%(w/v) PEG6000. crystallization drop: 4 mikroliter protein solution plus 2 mikroliter reservoir solution.
Resolution 1.16 Å R-free 0.185
9FBI Structure of human protein kinase CK2 catalytic subunit (CK2alpha', CSNK2A2 gene product) in complex with the cyclic peptidomimetic compound 12 discovered by high-throughput screening Deposited 2024-05-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–350（350 aa）
Not recorded NIO NICOTINIC ACID × 1 EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；protein solution: 90 mikroliter CK2alpha'-Cys336Ser solution (5 mg/ml in 500 mmol/l NaCl, 25 mmol/l Tris/HCl, pH 8.5) was mixed with 10 mikroliter 10 millimolar FMP37 in DMSO and incubated for 30 min. reservoir: 810 mmol/l LiCl, 100 mM Tris/HCl, pH 8.5, 28%(w/v) PEG6000. crystallization drop: 4 mikroliter protein solution plus 2 mikroliter reservoir solution.
Resolution 1.16 Å R-free 0.185
9GXY Crystal structure of protein kinase CK2 catalytic subunit (CSNK2A2 gene product) in complex with the dual CK2/HDAC inhibitor IOR-160 Deposited 2024-10-01 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S A1IKB 5-[[8-(oxidanylamino)-8-oxidanylidene-octyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；Original crystal: 47.5 microliter CK2alphaPrime mixed with 2.5 microliter of a 20 mM CX-4945 solution in DMSO to a final concentration of 5 mg per mL protein and 1 mM CX-4945. Reservoir (900 mM LiCl, 250 mM TRIS HCl, pH 8.5, 28 % PEG 6000) was mixed 1:2 with protein stock. Crystal were optimized by micro- and macroseeding. IOR-160 was introduced by back-soaking: 8 microliter reservoir were mixed for this with with 2 microliter of a 10 mM IOR-160 stock in DMSO. The crystal was soaked in 4 microliters of this solution of 72 hours.
Resolution 1.16 Å R-free 0.178
9H96 STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR MC11 Deposited 2024-10-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 A1ITG 1,2,3,4-tetrakis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；28 % (w/v) PEG 6000, 100 mM TRIS-HCl pH 8.5, 900 mM LiCl and 1 mM MB002, Growth and optimization by micro- and macroseeding. MC11 was introduced by backsoaking in a solution containing 2 mM MC11
Resolution 1.04 Å R-free 0.186
9HK5 Structure of a mutant of human protein kinase CK2alpha' that equals its isoenzyme CK2alpha in affinity to the regulatory subunit CK2beta Deposited 2024-12-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：P32V, V83I, T101I, C336S EDO 1,2-ETHANEDIOL × 2 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；protein stock solution: 5 mg/ml protein, 500 mM NaCl, 25 mM Tris/HCl, pH 8.5; protein/inhibitor mixture: 19 mikroliter protein stock solution plus 1 mikroliter 20 mM CX-4945 in DMSO; reservoir: 900 mM LiCL, 28 % (w/v) PEG 6000, 250 mM Tris/HCl, pH 8.5; crystallization drop: 2 mikroliter reservoir + 4 mikroliter protein/inhibitor mixture; initial crystals were optimized by micro seeding
Resolution 1.49 Å R-free 0.204
9IHG Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment C02 Deposited 2025-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S SYA 2,4,5-tris(fluoranyl)-3-methoxy-benzoic acid × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Niefind,K. 0000-0002-0183-6315 Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.08 Å R-free 0.157
9IHI Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D02 Deposited 2025-02-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S SY4 ~{N}-[5-azanyl-2,4-bis(fluoranyl)phenyl]propane-1-sulfonamide × 1 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.23 Å R-free 0.166
9Q8C Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment F02 Deposited 2025-03-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded T9Y ethyl 5-(trifluoromethyl)-1H-pyrazole-4-carboxylate × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.90 Å R-free 0.148
9Q8Q Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment E03 Deposited 2025-02-25 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S A1I4N 1-phenyl-1,3-diazinane-2,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.98 Å R-free 0.179
9Q9A Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment C06 and CX-4945 (Silmitasertib) Deposited 2025-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 A1I4V ~{N}-(3-chloranyl-4-methyl-phenyl)ethanamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.03 Å R-free 0.156
9Q9B Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment C07 and CX-4945 (Silmitasertib) Deposited 2025-02-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded VN9 3,4-dihydro-1~{H}-quinolin-2-one × 1 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.84 Å R-free 0.206
9Q9C Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D04 Deposited 2025-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S R9D methyl 4-fluoro-D-phenylalaninate × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.66 Å R-free 0.223
9Q9D Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D06 and CX-4945 (Silmitasertib) Deposited 2025-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 R9G (3-methoxyphenyl)(pyrrolidin-1-yl)methanone × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.89 Å R-free 0.159
9Q9G Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment D10 Deposited 2025-02-26 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S R9J 2-methyl-N-(4-methylphenyl)-L-alanine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.94 Å R-free 0.157
9QAB Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment E11 and CX-4945 (Silmitasertib) Deposited 2025-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S RA7 [2-(morpholin-4-yl)-1,3-thiazol-5-yl]methanol × 2 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.95 Å R-free 0.141
9QAG Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment F08 and CX-4945 (Silmitasertib) Deposited 2025-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 RBJ 4-[(methylamino)methyl]phenol × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.01 Å R-free 0.162
9QAK Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment G07 Deposited 2025-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S A1I5I 2-[(4-methyl-1,2,4-triazol-3-yl)sulfanyl]ethanoic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 0.98 Å R-free 0.175
9QB0 Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment H07 Deposited 2025-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S U8X ~{N}-(4-hydroxyphenyl)-2-pyrazol-1-yl-ethanamide × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.01 Å R-free 0.156
9QB6 Protein kinase CK2 catalytic subunit alpha' (CSNK2A2 gene product) in complex with F2X-Entry screen fragment H02 and CX-4945 (Silmitasertib) Deposited 2025-02-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S RDV 3-cyclopentyl-1-(piperazin-1-yl)propan-1-one × 1 3NG 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM CX-4945 and 5 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/CX-4945 mix Crystal optimization by micro- and macroseeding Ligand soaking: 100 mM ligand in 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.05 Å R-free 0.144
9QB9 CK2, catalytic subunit alpha' (CSNK2A2 gene product) in complex with a heparin-derived trisaccharide and the ATP-competitive inhibitor 4w Deposited 2025-03-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Mutation：C336S A1I5N 1,3-bis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Original reservoir: 900 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000 Protein mixture: 5 mg/mL CK2alpha Prime in 500 mM NaCl, 25 mM Tris HCl, pH 8.5, 1 mM 4w and 10 % DMSO Drop: 2 microliter reservoir, 4 microliter protein/4w mix Crystal optimization by micro- and macroseeding Desalting process: Step-wise replacement of original drop solution by 50 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO over 10 days Ligand soaking: 100 mM ligand in 50 mM LiCl, 250 mM Tris HCl, pH 8.5, 28 % PEG 6000, 5 % DMSO Equilibration for 24 h against new reservoir: 50 mM LiCl, 250 mM Tris HCl, pH 8.5, saturated PEG 6000
Resolution 1.19 Å R-free 0.175
9R57 Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 5,6-dibromo-1H-1,2,3-benzotriazole Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded 7M0 5,6-DIBROMOBENZOTRIAZOLE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Inititial drop: 5 mg per mL CK2alpha Prime with 1 mM MB002, 10 percent DMSO mixed in 2:1 ratio with reservoir (10 and 5 microliter). Optimization of crystal by microseeding and macroseeding. Complex formation by extensive purging with reservoir solution and extensive soaking at compounds saturation limit.
Resolution 1.10 Å R-free 0.150
9R5B Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 6,7-dibromo-4,5-difluoro-1H-1,2,3-benzotriazole Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded A1JCY 6,7-bis(bromanyl)-4,5-bis(fluoranyl)-1~{H}-benzotriazole × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 10 MICROLITERS OF the resulting solution WERE MIXED WITH 5 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against 6,7-dibromo-4,5-difluoro-1H-1,2,3-benzotriazole by an extensive soaking procedure of several steps.
Resolution 1.09 Å R-free 0.168
9R5C Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,7-dibromo-5,6-difluoro-1H-1,2,3-benzotriazole Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded A1JCZ 4,7-bis(bromanyl)-5,6-bis(fluoranyl)-1~{H}-benzotriazole × 1 4B0 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WERE MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 10 MICROLITERS OF the resulting solution WERE MIXED WITH 5 MICROLITERS OF RESERVOIR SOLUTION (900 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against 4,7-dibromo-5,6-difluoro-1H-1,2,3-benzotriazole by an extensive soaking procedure of several steps.
Resolution 1.04 Å R-free 0.164
9R5D Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 4,6-dibromo-5,7-difluoro-1H-1,2,3-benzotriazole Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 A1JC0 4,6-bis(bromanyl)-5,7-bis(fluoranyl)-1~{H}-benzotriazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；Reservoir was: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000. Protein/Ligand mix: 5 mg per mL CK2alpha Prime mixed with 2 mM ligand and 10 % DMSO. Drop: 2:1 mix of protein and ligand vs resevoir Optimization: Micro- and macroseeding
Resolution 1.02 Å R-free 0.193
9R5F Crystal structure of human protein kinase CK2 catalytic subunit (isoenzyme ck2alpha'; CSNK2A2 gene product) in complex with 5,6-dibromo-4,7-difluoro-1H-1,2,3-benzotriazole Deposited 2025-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–350（350 aa）
Not recorded A1JCX 5,6-bis(bromanyl)-4,7-bis(fluoranyl)-1~{H}-benzotriazole × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；Reservoir: 900 mM LiCl, 100 mM TRIS-HCl pH 8.5, 28 % PEG6000 Protein/ligand mix: 5 mg per mL Ck2alpha Prime including 2 mM ligand and 10 % DMSO Drop: 2:1 mix of protein/ligand vs reservoir optimization: Micro- and Macroseeding
Resolution 1.19 Å R-free 0.155

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View Construct and Data Evidence
UniProt name CSK22_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–339； UniProt 1–334 Author chain X； PDBConstruct 6–339； UniProt 1–334

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5y9m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5y9m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5y9m
Deposition date deposition_date2017-08-25
Structure title titleCrystal structure of CK2a2 form 3
Keywords keywordsprotein kinase, transferase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.54 Å
Radius of gyration Rg (electron density) rg_electron31.00 Å
Forward intensity I(0) i090951000.00
Molecular weight molecular_weight76875.0 kDa
Excluded volume excluded_volume96704 ų
Envelope volume envelope_volume120350 ų
Hydration-shell volume shell_volume32963 ų
Envelope diameter envelope_diameter105.6 Å
Shell Rg shell_rg37.14 Å
Envelope Rg envelope_rg30.89 Å
Shape Rg shape_rg31.00 Å
Total Rg total_rg31.52 Å
Total atoms total_atoms5430
Residues n_residues639
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.8 Å
Rg (real space) rg_real31.66 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real9.0950e+07
I(0) uncertainty (real space) i0_real_error1.4230e+06
Rg (reciprocal space) rg_reciprocal31.62 Å
I(0) (reciprocal space) i0_reciprocal90950000.0000
Solution quality estimate total_estimate0.8817
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.4 Å
Skewness Skewness skewness0.382
Kurtosis Kurtosis kurtosis-0.505
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24200000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.881
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5y9ma_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5y9mx_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id5y9mA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5y9mA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5y9mX01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5y9mX02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
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8. Citations (1)

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9. Files and Curves (10)