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4dgm

Crystal Structure of maize CK2 in complex with the inhibitor apigenin

Method: X-RAY DIFFRACTION Dmax: 70.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase II subunit alpha

Zea mays

UniProt P28523

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 A； UniProt 2–327 Not recorded EDO 1,2-ETHANEDIOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 AGI 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate, pH 8, VAPOR DIFFUSION, temperature 293K Resolution 1.65 Å R-free 0.252

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 4DGM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DAW CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPHA-SUBUNIT) AND MG-AMPPNP Deposited 1999-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：CATALYTIC SUBUNIT
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 3350, SODIUM ACETATE, TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.285
1DAY CRYSTAL STRUCTURE OF A BINARY COMPLEX OF PROTEIN KINASE CK2 (ALPHA-SUBUNIT) AND MG-GMPPNP Deposited 1999-11-01 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：CATALYTIC SUBUNIT
Not recorded MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；PEG 3350, SODIUM ACETATE, TRIS/HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.290
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. Deposited 2000-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–332（332 aa）
Chain B 1–332（332 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.16 Å R-free 0.289
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. Deposited 2000-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–332（332 aa）
Chain D 1–332（332 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 3.16 Å R-free 0.289
1F0Q CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT OF PROTEIN KINASE CK2 IN COMPLEX WITH THE NUCLEOTIDE COMPETITIVE INHIBITOR EMODIN Deposited 2000-05-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded EMO 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.63 Å R-free 0.273
1J91 Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the ATP-competitive inhibitor 4,5,6,7-tetrabromobenzotriazole Deposited 2001-05-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded TBS 4,5,6,7-TETRABROMOBENZOTRIAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.22 Å R-free 0.268
1J91 Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the ATP-competitive inhibitor 4,5,6,7-tetrabromobenzotriazole Deposited 2001-05-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–332（332 aa）
Not recorded TBS 4,5,6,7-TETRABROMOBENZOTRIAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, sodium acetate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.22 Å R-free 0.268
1JAM Crystal structure of apo-form of Z. Mays CK2 protein kinase alpha subunit Deposited 2001-05-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；287 K；30% PEG 4000, 200 mM sodium acetate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 287K
Resolution 2.18 Å R-free 0.248
1LP4 Crystal structure of a binary complex of the catalytic subunit of protein kinase CK2 with Mg-AMPPNP Deposited 2002-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；PEG3350, SODIUM ACETATE, TRIS/HCL, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.86 Å R-free 0.244
1LPU Low Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays Deposited 2002-05-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded BEN BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；PEG3350, Tris/HCl, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.86 Å R-free 0.248
1LR4 Room Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays Deposited 2002-05-14 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded BEN BENZAMIDINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.237
1M2P Crystal structure of 1,8-di-hydroxy-4-nitro-anthraquinone/CK2 kinase complex Deposited 2002-06-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–326（325 aa） Fragment：Catlytic subunit
Not recorded HNA 1,8-DI-HYDROXY-4-NITRO-ANTHRAQUINONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.243
1M2Q Crystal structure of 1,8-di-hydroxy-4-nitro-xanten-9-one/CK2 kinase complex Deposited 2002-06-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：Catlytic subunit
Not recorded MNX 1,8-DI-HYDROXY-4-NITRO-XANTHEN-9-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.79 Å R-free 0.232
1M2R Crystal structure of 5,8-di-amino-1,4-di-hydroxy-anthraquinone/CK2 kinase complex Deposited 2002-06-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：catalytic subunit
Not recorded MNY 5,8-DI-AMINO-1,4-DIHYDROXY-ANTHRAQUINONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.216
1OM1 Crystal structure of maize CK2 alpha in complex with IQA Deposited 2003-02-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded IQA (5-OXO-5,6-DIHYDRO-INDOLO[1,2-A]QUINAZOLIN-7-YL)-ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；PEG 4000, SODIUM ACETATE, TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.68 Å R-free 0.227
1ZOE Crystal structure of protein kinase CK2 in complex with TBB-derivatives inhibitors Deposited 2005-05-13 Different construct 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 1–332（332 aa）
Not recorded CL CHLORIDE ION × 2 K25 4,5,6,7-TETRABROMO-N,N-DIMETHYL-1H-BENZIMIDAZOL-2-AMINE × 2 DMS DIMETHYL SULFOXIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.77 Å R-free 0.277
1ZOG Crystal structure of protein kinase CK2 in complex with TBB-derivatives Deposited 2005-05-13 Different construct 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 1–332（332 aa）
Not recorded K37 4,5,6,7-TETRABROMO-2-(METHYLSULFANYL)-1H-BENZIMIDAZOLE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.294
1ZOH Crystal structure of protein kinase CK2 in complex with TBB-derivatives inhibitors Deposited 2005-05-13 Different construct 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 1–332（332 aa）
Not recorded NA SODIUM ION × 2 CL CHLORIDE ION × 4 K44 5,6,7,8-TETRABROMO-1-METHYL-2,3-DIHYDRO-1H-IMIDAZO[1,2-A]BENZIMIDAZOLE × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；PEG 4000, Sodium Acetate, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.81 Å R-free 0.221
2OXD Protein kinase CK2 in complex with tetrabromobenzoimidazole K17, K22 and K32 inhibitors Deposited 2007-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded K32 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 2.30 Å R-free 0.273
2OXX Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 Deposited 2007-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded K22 4,5,6,7-TETRABROMO-1H,3H-BENZIMIDAZOL-2-THIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M TrisHCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.270
2OXY Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 Deposited 2007-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded K17 4,5,6,7-TETRABROMO-BENZIMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.81 Å R-free 0.269
2OXY Protein kinase CK2 in complex with tetrabromobenzoimidazole derivatives K17, K22 and K32 Deposited 2007-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–332（332 aa）
Not recorded K17 4,5,6,7-TETRABROMO-BENZIMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10-20% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.81 Å R-free 0.269
2PVH Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P19 N,N'-DIPHENYLPYRAZOLO[1,5-A][1,3,5]TRIAZINE-2,4-DIAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；18% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.20 Å R-free 0.236
2PVJ Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P44 2-(CYCLOHEXYLMETHYLAMINO)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；12% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.70 Å R-free 0.218
2PVK Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P45 2-(4-CHLOROBENZYLAMINO)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.90 Å R-free 0.244
2PVL Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P55 2-(4-ETHYLPIPERAZIN-1-YL)-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.20M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 1.90 Å R-free 0.289
2PVM Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P29 4-(2-(1H-IMIDAZOL-4-YL)ETHYLAMINO)-2-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZINE-8-CARBONITRILE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；12% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.00 Å R-free 0.225
2PVN Structure-Based Design of Pyrazolo[1,5-a][1,3,5]triazine Derivatives as Potent Inhibitors of Protein Kinase CK2 Deposited 2007-05-09 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P63 N-(3-(8-CYANO-4-(PHENYLAMINO)PYRAZOLO[1,5-A][1,3,5]TRIAZIN-2-YLAMINO)PHENYL)ACETAMIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；16% PEG 4000, 0.10M Sodium Acetate, 0.10M TrisHCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.00 Å R-free 0.308
2QC6 Protein kinase CK2 in complex with DBC Deposited 2007-06-19 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 1–332（332 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) G12 3,8-DIBROMO-7-HYDROXY-4-METHYL-2H-CHROMEN-2-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；10-20% PEG4000, 0.2 M Sodium Acetate, 0.1 M Tris, pH 8, VAPOR DIFFUSION, temperature 293.0K
Resolution 1.85 Å R-free 0.268
3BE9 Structure-based design and synthesis of novel macrocyclic pyrazolo[1,5-a] [1,3,5]triazine compounds as potent inhibitors of protein kinase CK2 and their anticancer activities Deposited 2007-11-16 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 1–332（332 aa）
Mutation：V256A Non-standard monomer：Yes (specific site not provided by mmCIF) P04 19-(cyclopropylamino)-4,6,7,15-tetrahydro-5H-16,1-(azenometheno)-10,14-(metheno)pyrazolo[4,3-o][1,3,9]triazacyclohexadecin-8(9H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；297 K；14% PEG 4000, 0.05M Sodium Acetate, 0.10M TRISHCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Resolution 2.00 Å R-free 0.228
3FL5 Protein kinase CK2 in complex with the inhibitor Quinalizarin Deposited 2008-12-18 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 1–332（332 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PEG DI(HYDROXYETHYL)ETHER × 1 TXQ 1,2,5,8-tetrahydroxyanthracene-9,10-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 4000, 200mM Na-acetate, 100mM Na-HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.235
3KXG Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor 3,4,5,6,7-pentabromo-1H-indazole (K64) Deposited 2009-12-03 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 2–328（327 aa） Fragment：ALPHA SUBUNIT
Non-standard monomer：Yes (specific site not provided by mmCIF) K6X 3,4,5,6,7-pentabromo-1H-indazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.263
3KXH Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor (2-dymethylammino-4,5,6,7-tetrabromobenzoimidazol-1yl-acetic acid (K66) Deposited 2009-12-03 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 2–328（327 aa） Fragment：ALPHA SUBUNIT
Non-standard monomer：Yes (specific site not provided by mmCIF) K66 [4,5,6,7-tetrabromo-2-(dimethylamino)-1H-benzimidazol-1-yl]acetic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.70 Å R-free 0.266
3KXM Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor K74 Deposited 2009-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：ALPHA SUBUNIT
Not recorded K74 N-methyl-2-[(4,5,6,7-tetrabromo-1-methyl-1H-benzimidazol-2-yl)sulfanyl]acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.282
3KXN Crystal structure of Z. mays CK2 kinase alpha subunit in complex with the inhibitor tetraiodobenzimidazole (K88) Deposited 2009-12-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–328（327 aa） Fragment：ALPHA SUBUNIT
Not recorded K8X 4,5,6,7-tetraiodo-1H-benzimidazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.00 Å R-free 0.264
3PVG Crystal structure of Z. mays CK2 alpha subunit in complex with the inhibitor 4,5,6,7-tetrabromo-1-carboxymethylbenzimidazole (K68) Deposited 2010-12-07 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 2–332（331 aa） Fragment：alpha subunit
Non-standard monomer：Yes (specific site not provided by mmCIF) K68 (4,5,6,7-tetrabromo-1H-benzimidazol-1-yl)acetic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M Na-acetate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.50 Å R-free 0.211
3PWD Crystal structure of maize CK2 in complex with NBC (Z1) Deposited 2010-12-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded CZ0 8-hydroxy-4-methyl-9-nitro-2H-benzo[g]chromen-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K
Resolution 2.20 Å R-free 0.230
3PZH Crystal structure of maize CK2 alpha in complex with emodin at 1.92 A resolution Deposited 2010-12-14 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 1–332（332 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EMO 3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE × 1 ACT ACETATE ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；20% PEG 4000, 0.2M sodium acetate, 0.1M TrisHCl, pH 8, vapor diffusion, sitting drop, temperature 293K
Resolution 1.92 Å R-free 0.209
4ANM Complex of CK2 with a CDC7 inhibitor Deposited 2012-03-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–332（331 aa） Fragment：KINASE DOMAIN, RESIDUES 2-332
Not recorded WUL 8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；20% PEG4K, 200 MM NAOAC, 100 MM TRIS, PH 8.0
Resolution 1.70 Å R-free 0.202
4DGN Crystal Structure of maize CK2 in complex with the inhibitor luteolin Deposited 2012-01-26 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–327（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) LU2 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate, pH 8, VAPOR DIFFUSION, temperature 293K
Resolution 1.75 Å R-free 0.214
4RLK Crystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate Deposited 2014-10-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–332（332 aa）
Not recorded GOL GLYCEROL × 3 ACT ACETATE ION × 2 E91 4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Reservoir: 20 % PEG 4000, 0.2 M sodium acetate, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.24 Å R-free 0.175
6QS5 Crystal Structure of maize CK2 in complex with tyrphostin AG99 Deposited 2019-02-20 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–326（325 aa）
Not recorded JGB (~{E})-3-[3,4-bis(oxidanyl)phenyl]-2-cyano-prop-2-enamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.1 M Tris-HCl, 10-20% PEG 4000, 0.2 M Na-acetate
Resolution 1.96 Å R-free 0.219

39 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSK2A_MAIZE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–326； UniProt 2–327

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 4dgm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4dgm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4dgm
Deposition date deposition_date2012-01-26
Structure title titleCrystal Structure of maize CK2 in complex with the inhibitor apigenin
Keywords keywordsprotein kinase, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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_guinier21.59 Å
Radius of gyration Rg (electron density) rg_electron20.28 Å
Forward intensity I(0) i024706600.00
Molecular weight molecular_weight39164.0 kDa
Excluded volume excluded_volume49520 ų
Envelope volume envelope_volume56603 ų
Hydration-shell volume shell_volume23000 ų
Envelope diameter envelope_diameter70.1 Å
Shell Rg shell_rg27.35 Å
Envelope Rg envelope_rg20.64 Å
Shape Rg shape_rg20.28 Å
Total Rg total_rg21.24 Å
Total atoms total_atoms2766
Residues n_residues326
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 dmax70.4 Å
Rg (real space) rg_real21.50 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.4710e+07
I(0) uncertainty (real space) i0_real_error3.1650e+05
Rg (reciprocal space) rg_reciprocal21.52 Å
I(0) (reciprocal space) i0_reciprocal24710000.0000
Solution quality estimate total_estimate0.8881
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9 Å
Skewness Skewness skewness0.254
Kurtosis Kurtosis kurtosis-0.350
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6968000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4dgma_
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 (2 domains)

Domain ID domain_id4dgmA01
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_id4dgmA02
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)