4rlk

Crystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate

Method: X-RAY DIFFRACTION D_max: 71.2 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase II subunit alpha

Zea mays

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 1–332	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

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 4RLK	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
4DGM Crystal Structure of maize CK2 in complex with the inhibitor apigenin Deposited 2012-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–327（326 aa）	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
4DGN Crystal Structure of maize CK2 in complex with the inhibitor luteolin Deposited 2012-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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
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 1–332； UniProt 1–332

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4rlk
Deposition date deposition_date	2014-10-17
Structure title title	Crystal structure of Z. mays CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate
Keywords keywords	TRANSFERASE, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.66 Å
Radius of gyration Rg (electron density) rg_electron	20.34 Å
Forward intensity I(0) i0	24940800.00
Molecular weight molecular_weight	39319.0 kDa
Excluded volume excluded_volume	49676 Å³
Envelope volume envelope_volume	57011 Å³
Hydration-shell volume shell_volume	23105 Å³
Envelope diameter envelope_diameter	71.6 Å
Shell Rg shell_rg	27.42 Å
Envelope Rg envelope_rg	20.72 Å
Shape Rg shape_rg	20.34 Å
Total Rg total_rg	21.30 Å
Total atoms total_atoms	2778
Residues n_residues	327
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	71.2 Å
Rg (real space) rg_real	21.57 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.4940e+07
I(0) uncertainty (real space) i0_real_error	2.8360e+05
Rg (reciprocal space) rg_reciprocal	21.59 Å
I(0) (reciprocal space) i0_reciprocal	24940000.0000
Solution quality estimate total_estimate	0.8857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.258
Kurtosis Kurtosis kurtosis	-0.335
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7383000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Casein kinase II subunit alpha
Molecular weight formula_weight	39291.2 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3228

MSKARVYADVNVLRPKEYWDYEALTVQWGEQDDYEVVRKVGRGKYSEVFEGINVNNNEKCIIKILKPVKKKKIKREIKILQNLCGGPNIVKLLDIVRDQHSKTPSLIFEYVNNTDFKVLYPTLTDYDIRYYIYELLKALDYCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNHDQLVKIAKVLGTDGLNVYLNKYRIELDPQLEALVGRHSRKPWLKFMNADNQHLVSPEAIDFLDKLLRYDHQERLTALEAMTHPYFQQVRAAENSRTRA

来源 Source

来源生物 organism	Zea mays
通用名 common_name	maize
NCBI Class编号 ncbi_taxonomy_id	4577
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid
Molecular weight formula_weight	326.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	324

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4rlka_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id	4rlkA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4rlkA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

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8. Citations (1)

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Unit-cell length a length_a	142.748 Å
Unit-cell length b length_b	59.683 Å
Unit-cell length c length_c	44.884 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.96 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.240 Å
Low-resolution limit resolution_low	43.740 Å
R factor r_factor	0.1449
R_work r_work	0.1433
R_free r_free	0.1753

fit	/app/data/saxs_computation/rl/4rlk/4rlk.fit
pddf	/app/data/pr_computation/rl/4rlk/4rlk.pr.out
profile	/app/data/saxs_computation/rl/4rlk/4rlk.dat