Current Protein Identity：P19784
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | 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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 |
| 5Y9M Crystal structure of CK2a2 form 3 Deposited 2017-08-25 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain X
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；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 |
| 5Y9M Crystal structure of CK2a2 form 3 Deposited 2017-08-25 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–334（334 aa）
Fragment：UNP residues 1-334
|
Not recorded | 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 |
| 5YF9 Crystal structure of CK2a2 form-2 Deposited 2017-09-20 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 |