Cyclin-dependent kinase 12
Homo sapiens
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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 717–1036 | Non-standard monomer：Yes (specific site not provided by mmCIF) | Cyclin-K × 1 （O75909） MG MAGNESIUM ION × 1 CJM 2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl)methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol × 1 EDO 1,2-ETHANEDIOL × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2 | Resolution 3.06 Å R-free 0.212 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain C； UniProt 717–1036 | Non-standard monomer：Yes (specific site not provided by mmCIF) | Cyclin-K × 1 （O75909） MG MAGNESIUM ION × 1 CJM 2-[(2S)-1-(6-{[(4,5-difluoro-1H-benzimidazol-2-yl)methyl]amino}-9-ethyl-9H-purin-2-yl)piperidin-2-yl]ethan-1-ol × 1 EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2 | Resolution 3.06 Å R-free 0.212 |
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 6B3E | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4CXA Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP Deposited 2014-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
715–1052（338 aa）
Fragment：KINASE DOMAIN, RESIDUES 715-1052
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；0.15M DL-MALIC ACID, 20% PEG3350, pH 7
|
Resolution 3.15 Å R-free 0.279 |
| 4CXA Crystal structure of the human CDK12-cyclin K complex bound to AMPPNP Deposited 2014-04-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
715–1052（338 aa）
Fragment：KINASE DOMAIN, RESIDUES 715-1052
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；0.15M DL-MALIC ACID, 20% PEG3350, pH 7
|
Resolution 3.15 Å R-free 0.279 |
| 4NST Crystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride Deposited 2013-11-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
714–1063（350 aa）
Fragment：Protein kinase domain, residues 714-1063
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.240 |
| 4NST Crystal structure of human Cdk12/Cyclin K in complex with ADP-aluminum fluoride Deposited 2013-11-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
714–1063（350 aa）
Fragment：Protein kinase domain, residues 714-1063
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 20.5% PEG 3350, 0.4 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.20 Å R-free 0.240 |
| 4UN0 Crystal structure of the human CDK12-cyclinK complex Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
715–1038（324 aa）
Fragment：KINASE DOMAIN, RESIDUES 715-1038
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；20% PEG3350, 10% ETGLY, 0.1M BISTRIS PROPANE PH6.5, 0.2M SODIUM NITRATE
|
Resolution 3.15 Å R-free 0.271 |
| 4UN0 Crystal structure of the human CDK12-cyclinK complex Deposited 2014-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
715–1038（324 aa）
Fragment：KINASE DOMAIN, RESIDUES 715-1038
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；20% PEG3350, 10% ETGLY, 0.1M BISTRIS PROPANE PH6.5, 0.2M SODIUM NITRATE
|
Resolution 3.15 Å R-free 0.271 |
| 5ACB Crystal Structure of the Human Cdk12-Cyclink Complex Deposited 2015-08-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
715–1052（338 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 5I1 N-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
10% PEG8000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH7.0
|
Resolution 2.70 Å R-free 0.262 |
| 5ACB Crystal Structure of the Human Cdk12-Cyclink Complex Deposited 2015-08-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
715–1052（338 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | 5I1 N-[4-[(3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]piperidin-1-yl]carbonylphenyl]-4-(dimethylamino)butanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
10% PEG8000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH7.0
|
Resolution 2.70 Å R-free 0.262 |
| 6CKX Structure of CDK12/CycK in complex with a small molecule inhibitor N-(4-(1-methyl-1H-pyrazol-4-yl)phenyl)-N-((1r,4r)-4-(quinazolin-2-ylamino)cyclohexyl)acetamide Deposited 2018-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
714–1063（350 aa）
Fragment：UNP RESIDUES 713-1062
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 2 8M1 N-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-{trans-4-[(quinazolin-2-yl)amino]cyclohexyl}acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES (PH 6.5), 18% PEG 3350,
0.2 M MGCL2, AND 1 MM SARCOSINE, VAPOR DIFFUSION, HANGING DROP,
TEMPERATURE 297K
|
Resolution 2.80 Å R-free 0.251 |
| 6CKX Structure of CDK12/CycK in complex with a small molecule inhibitor N-(4-(1-methyl-1H-pyrazol-4-yl)phenyl)-N-((1r,4r)-4-(quinazolin-2-ylamino)cyclohexyl)acetamide Deposited 2018-03-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
714–1063（350 aa）
Fragment：UNP RESIDUES 713-1062
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 1 8M1 N-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-{trans-4-[(quinazolin-2-yl)amino]cyclohexyl}acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M HEPES (PH 6.5), 18% PEG 3350,
0.2 M MGCL2, AND 1 MM SARCOSINE, VAPOR DIFFUSION, HANGING DROP,
TEMPERATURE 297K
|
Resolution 2.80 Å R-free 0.251 |
| 6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Mutation：K965R Non-standard monomer：Yes (specific site not provided by mmCIF) | RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
|
Resolution 3.46 Å R-free 0.220 |
| 6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Mutation：K965R Non-standard monomer：Yes (specific site not provided by mmCIF) | RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
|
Resolution 3.46 Å R-free 0.220 |
| 6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Mutation：K965R Non-standard monomer：Yes (specific site not provided by mmCIF) | RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
|
Resolution 3.46 Å R-free 0.220 |
| 7NXK Crystal structure of human Cdk12/Cyclin K in complex with the inhibitor BSJ-01-175 Deposited 2021-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
714–1063（350 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UUB (E)-N-[4-[(1R,3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]cyclohexyl]oxyphenyl]-4-(dimethylamino)but-2-enamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES, pH 6.0, 30% PEGmixture (medium weight pegs), 0.3 M NDSB, 0.2 M MgCl2.
|
Resolution 3.00 Å R-free 0.264 |
| 7NXK Crystal structure of human Cdk12/Cyclin K in complex with the inhibitor BSJ-01-175 Deposited 2021-03-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
714–1063（350 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | UUB (E)-N-[4-[(1R,3R)-3-[[5-chloranyl-4-(1H-indol-3-yl)pyrimidin-2-yl]amino]cyclohexyl]oxyphenyl]-4-(dimethylamino)but-2-enamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES, pH 6.0, 30% PEGmixture (medium weight pegs), 0.3 M NDSB, 0.2 M MgCl2.
|
Resolution 3.00 Å R-free 0.264 |
| 8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
|
Resolution 2.98 Å R-free 0.218 |
| 8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
|
Resolution 2.98 Å R-free 0.218 |
| 8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
|
Resolution 2.98 Å R-free 0.218 |
| 8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 12 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.13 Å R-free 0.217 |
| 8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 16 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.13 Å R-free 0.217 |
| 8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 13 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.13 Å R-free 0.217 |
| 8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 6 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
|
Resolution 3.42 Å R-free 0.213 |
| 8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
|
Resolution 3.42 Å R-free 0.213 |
| 8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 9 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
|
Resolution 3.42 Å R-free 0.213 |
| 8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.09 Å R-free 0.223 |
| 8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.09 Å R-free 0.223 |
| 8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.09 Å R-free 0.223 |
| 8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.13 Å R-free 0.220 |
| 8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.13 Å R-free 0.220 |
| 8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.13 Å R-free 0.220 |
| 8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
|
Resolution 3.45 Å R-free 0.249 |
| 8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
|
Resolution 3.45 Å R-free 0.249 |
| 8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
|
Resolution 3.45 Å R-free 0.249 |
| 8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
|
Resolution 3.25 Å R-free 0.219 |
| 8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 2 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
|
Resolution 3.25 Å R-free 0.219 |
| 8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
|
Resolution 3.25 Å R-free 0.219 |
| 8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.51 Å R-free 0.223 |
| 8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.51 Å R-free 0.223 |
| 8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
|
Resolution 3.51 Å R-free 0.223 |
| 8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
|
Resolution 3.19 Å R-free 0.225 |
| 8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 3 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
|
Resolution 3.19 Å R-free 0.225 |
| 8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 4 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
|
Resolution 3.19 Å R-free 0.225 |
| 8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
|
Resolution 3.42 Å R-free 0.237 |
| 8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 3 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
|
Resolution 3.42 Å R-free 0.237 |
| 8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
|
Resolution 3.42 Å R-free 0.237 |
| 8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.85 Å R-free 0.224 |
| 8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 1 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 CIT CITRIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.85 Å R-free 0.224 |
| 8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.85 Å R-free 0.224 |
| 8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 10 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.20 Å R-free 0.220 |
| 8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 15 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.20 Å R-free 0.220 |
| 8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 14 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.20 Å R-free 0.220 |
| 8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 12 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
|
Resolution 3.25 Å R-free 0.213 |
| 8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 16 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
|
Resolution 3.25 Å R-free 0.213 |
| 8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 15 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
|
Resolution 3.25 Å R-free 0.213 |
| 8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 12 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.30 Å R-free 0.220 |
| 8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.30 Å R-free 0.220 |
| 8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.30 Å R-free 0.220 |
| 8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
|
Resolution 3.53 Å R-free 0.231 |
| 8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
|
Resolution 3.53 Å R-free 0.231 |
| 8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 3 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
|
Resolution 3.53 Å R-free 0.231 |
| 8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.79 Å R-free 0.232 |
| 8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.79 Å R-free 0.232 |
| 8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.79 Å R-free 0.232 |
| 8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.50 Å R-free 0.221 |
| 8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.50 Å R-free 0.221 |
| 8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.50 Å R-free 0.221 |
| 8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.62 Å R-free 0.206 |
| 8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 4 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.62 Å R-free 0.206 |
| 8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.62 Å R-free 0.206 |
| 8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.41 Å R-free 0.210 |
| 8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.41 Å R-free 0.210 |
| 8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
|
Resolution 3.41 Å R-free 0.210 |
| 8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1052（341 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.40 Å R-free 0.215 |
| 8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1052（341 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.40 Å R-free 0.215 |
| 8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1052（341 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 9 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.40 Å R-free 0.215 |
| 8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 11 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.36 Å R-free 0.212 |
| 8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 15 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.36 Å R-free 0.212 |
| 8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 13 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.36 Å R-free 0.212 |
| 8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 10 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.08 Å R-free 0.211 |
| 8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.08 Å R-free 0.211 |
| 8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.08 Å R-free 0.211 |
| 8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 9 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.58 Å R-free 0.219 |
| 8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.58 Å R-free 0.219 |
| 8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 10 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
|
Resolution 3.58 Å R-free 0.219 |
| 8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 11 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
|
Resolution 3.41 Å R-free 0.223 |
| 8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 22 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
|
Resolution 3.41 Å R-free 0.223 |
| 8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 24 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
|
Resolution 3.41 Å R-free 0.223 |
| 8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
|
Resolution 3.20 Å R-free 0.216 |
| 8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
|
Resolution 3.20 Å R-free 0.216 |
| 8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
|
Resolution 3.20 Å R-free 0.216 |
| 8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.64 Å R-free 0.234 |
| 8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 10 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.64 Å R-free 0.234 |
| 8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.64 Å R-free 0.234 |
| 8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 5 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.26 Å R-free 0.228 |
| 8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.26 Å R-free 0.228 |
| 8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
|
Resolution 3.26 Å R-free 0.228 |
| 8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 7 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
|
Resolution 3.25 Å R-free 0.217 |
| 8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 6 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
|
Resolution 3.25 Å R-free 0.217 |
| 8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
712–1051（340 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 8 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
|
Resolution 3.25 Å R-free 0.217 |
| 8P81 Crystal structure of human Cdk12/Cyclin K in complex with inhibitor SR-4835 Deposited 2023-05-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
714–1063（350 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；0.1 M MOPS pH 6.5, 30% PEG mix, 0.1 M NDSB
|
Resolution 2.68 Å R-free 0.255 |
| 9FMR Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835 Deposited 2024-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
714–1063（350 aa）
Chain E
714–1063（350 aa）
Chain H
714–1063（350 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；283 K；1 M potassium citrate and 15% glycerol
|
Resolution 3.90 Å R-free 0.250 |
| 9JK1 Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118 Deposited 2024-09-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
715–1052（338 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 2 A1EB3 N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris, pH 5.8, 21.5% PEG 3350, 0.4 M MgCl2
|
Resolution 2.72 Å R-free 0.267 |
| 9JK1 Crystal structure of CDK12/Cyclin K in complex with covalent inhibitor YJZ5118 Deposited 2024-09-14 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
715–1052（338 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | A1EB3 N-[5-[[4-[(5-cyanopyridin-2-yl)amino]cyclohexyl]-[(phenylmethyl)carbamoyl]amino]-2-[4-(dimethylamino)piperidin-1-yl]phenyl]propanamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Bis-Tris, pH 5.8, 21.5% PEG 3350, 0.4 M MgCl2
|
Resolution 2.72 Å R-free 0.267 |
38 other PDB entries and 103 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CDK12_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–320； UniProt 717–1036 Author chain C； PDBConstruct 1–320； UniProt 717–1036 |
