Current Protein Identity：P50613
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
|
Resolution 3.02 Å R-free 0.288 |
| 1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
|
Resolution 3.02 Å R-free 0.288 |
| 1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
|
Resolution 3.02 Å R-free 0.288 |
| 1UA2 Crystal Structure of Human CDK7 Deposited 2004-08-11 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ATP ADENOSINE-5'-TRIPHOSPHATE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Na Citrate, Na Acetate, PEG 4000, glycerol, NDSB201, ATP, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K
|
Resolution 3.02 Å R-free 0.288 |
| 6O9L Human holo-PIC in the closed state Deposited 2019-03-14 | Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.20 Å |
| 6XBZ Structure of the human CDK-activating kinase Deposited 2020-06-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6XD3 Structure of the human CAK in complex with THZ1 Deposited 2020-06-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7B5O Cryo-EM structure of the human CAK bound to ICEC0942 at 2.5 Angstroms resolution Deposited 2020-12-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.50 Å |
| 7B5Q Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) Deposited 2020-12-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.50 Å |
| 7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 | Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric（51） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 | Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric（51） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16 | Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric（76） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16 | Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric（76） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.13 Å |
| 7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 | Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric（56） Consistent with all polymers |
Chain e
1–346（346 aa）
|
Not recorded | MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15 | Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric（58） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20 | Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric（42） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Mutation：0 | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14 | Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric（40） Consistent with all polymers |
Chain 8
1–346（346 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21 | Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric（87） Consistent with all polymers |
Chain HI
1–346（346 aa）
|
Mutation：K41A | ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.04 Å |
| 8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21 | Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric（87） Consistent with all polymers |
Chain HI
1–346（346 aa）
|
Mutation：K41A | ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.16 Å |
| 8ORM Cryo-EM structure of CAK-THZ1 Deposited 2023-04-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P4Z Crystal structure of the human CDK7 kinase domain in complex with LDC4297 Deposited 2023-05-23 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
10–311（302 aa）
|
Not recorded | WZ8 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 GOL GLYCEROL × 2 PGE TRIETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M ammonium acetate, 0.1 M sodium citrate, 12% w/v PEG 3350, 0.2 M NDSB-201
|
Resolution 2.75 Å R-free 0.251 |
| 8P4Z Crystal structure of the human CDK7 kinase domain in complex with LDC4297 Deposited 2023-05-23 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
10–311（302 aa）
|
Not recorded | WZ8 2-[(3R)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 GOL GLYCEROL × 6 1PE PENTAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M ammonium acetate, 0.1 M sodium citrate, 12% w/v PEG 3350, 0.2 M NDSB-201
|
Resolution 2.75 Å R-free 0.251 |
| 8P6V Cryo-EM structure of CAK in complex with inhibitor ICEC0942 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P6W Cryo-EM structure of CAK in complex with inhibitor BS-181 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X2H ~{N}5-(6-azanylhexyl)-~{N}7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P6X Cryo-EM structure of CAK in complex with inhibitor BS-194 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | NS9 (2S,3S)-3-{[7-(benzylamino)-3-(1-methylethyl)pyrazolo[1,5-a]pyrimidin-5-yl]amino}butane-1,2,4-triol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P6Y Cryo-EM structure of CAK in complex with nucleotide analogue ATPgS Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P6Z Cryo-EM structure of CAK in complex with inhibitor ICEC0510-R Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X4L N7-(phenylmethyl)-3-propan-2-yl-N5-[(3R)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 8P70 Cryo-EM structure of CAK in complex with inhibitor ICEC0510-S Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X4Q N7-(phenylmethyl)-3-propan-2-yl-N5-[(3S)-pyrrolidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.00 Å |
| 8P71 Cryo-EM structure of CAK in complex with inhibitor ICEC0574 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X4F (3R,4S)-4-[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]pyrrolidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.00 Å |
| 8P72 Cryo-EM structure of CAK in complex with inhibitor ICEC0768 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X2Z ~{N}7-(phenylmethyl)-~{N}5-[(3~{S})-piperidin-3-yl]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P73 Cryo-EM structure of CAK in complex with inhibitor ICEC0829 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X50 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 X58 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidine-3,4-diol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.00 Å |
| 8P74 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-up conformation) Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 8P75 Cryo-EM structure of CAK in complex with inhibitor ICEC0880 (ring-down conformation) Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X3Z (2S,3S)-3-[[7-[(2-bromophenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]butane-1,2,4-triol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.00 Å |
| 8P76 Cryo-EM structure of CAK in complex with inhibitor ICEC0914 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | X1W N5-[(3S,4R)-4-phenylmethoxypyrrolidin-3-yl]-N7-(phenylmethyl)-3-propan-2-yl-pyrazolo[1,5-a]pyrimidine-5,7-diamine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.00 Å |
| 8P77 Cryo-EM structure of CAK in complex with inhibitor ICEC0943 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | I73 (3S,4S)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.80 Å |
| 8P78 Cryo-EM structure of CAK in complex with inhibitor dinaciclib Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | 1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8P79 Cryo-EM structure of CAK with averaged inhibitor density Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；Structure obtained by combining data from six samples of CAK bound to different non-covalent inhibitors. Four samples contained 5 mM beta-mercaptoethanol and two samples did not.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.70 Å |
| 8P7L Cryo-EM structure of CDK7 subunit of CAK in complex with inhibitor LDC4297 Deposited 2023-05-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | WD9 2-[(3S)-piperidin-3-yl]oxy-8-propan-2-yl-N-[(2-pyrazol-1-ylphenyl)methyl]pyrazolo[1,5-a][1,3,5]triazin-4-amine × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 8PLZ Cryo-EM structure of CAK in complex with inhibitor CT7030 Deposited 2023-06-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ZQ6 (3~{R},4~{R})-4-[[[7-[(2-methoxyphenyl)methylamino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.90 Å |
| 8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
|
Resolution 2.15 Å R-free 0.241 |
| 8PYR Crystal structure of the dual T-loop phosphorylated Cdk7/CycH/Mat1 complex Deposited 2023-07-26 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
1–346（346 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；288 K；0.1 M Hepes (pH 7.0), 12% (v/w) medium weight PEG mix of PEG6K and PEG4K, 10% ethylene-glycol, and 0.2 M NDSB
|
Resolution 2.15 Å R-free 0.241 |
| 8R99 A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Mutation：W132R, S164D, T170E | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；.1M (NH4)3 citrate
.2M NDSB-201
15.2% PEG 3350
|
Resolution 1.81 Å R-free 0.220 |
| 8R9A A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | PEG DI(HYDROXYETHYL)ETHER × 1 I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；.2M Na2HPO4
20% PEG 3350
|
Resolution 1.71 Å R-free 0.294 |
| 8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–326（326 aa）
|
Mutation：S164D, T170E, del327-346 | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
|
Resolution 2.21 Å R-free 0.243 |
| 8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–326（326 aa）
|
Mutation：S164D, T170E, del327-346 | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
|
Resolution 2.21 Å R-free 0.243 |
| 8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain C
1–326（326 aa）
|
Mutation：S164D, T170E, del327-346 | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
|
Resolution 2.21 Å R-free 0.243 |
| 8R9B A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain D
1–326（326 aa）
|
Mutation：S164D, T170E, del327-346 | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；19% 2-propanol, 5% glycerol, 19%PEG4K, 0.095M Na3citrate pH5.6/HCl
|
Resolution 2.21 Å R-free 0.243 |
| 8R9O A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | YN3 ~{N}-[(1~{S})-2-(dimethylamino)-1-phenyl-ethyl]-6,6-dimethyl-3-[[4-(propanoylamino)phenyl]carbonylamino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate
15% PEG 3350
|
Resolution 2.22 Å R-free 0.344 |
| 8R9O A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | YN3 ~{N}-[(1~{S})-2-(dimethylamino)-1-phenyl-ethyl]-6,6-dimethyl-3-[[4-(propanoylamino)phenyl]carbonylamino]-1,4-dihydropyrrolo[3,4-c]pyrazole-5-carboxamide × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate
15% PEG 3350
|
Resolution 2.22 Å R-free 0.344 |
| 8R9S A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 YPK [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% Glycerol
.02M KNa tartrate
.02M NH4 acetate
.02M Na formate
.02M Na oxamate
.02M Na3 citrate
10% PEG 4000
.1M pH=7.5 MOPS/NaHEPES
|
Resolution 2.78 Å R-free 0.296 |
| 8R9S A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | PE3 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL × 2 YPK [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；20% Glycerol
.02M KNa tartrate
.02M NH4 acetate
.02M Na formate
.02M Na oxamate
.02M Na3 citrate
10% PEG 4000
.1M pH=7.5 MOPS/NaHEPES
|
Resolution 2.78 Å R-free 0.296 |
| 8R9U A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate
15% PEG 3350
|
Resolution 1.94 Å R-free 0.340 |
| 8R9U A soakable crystal form of human CDK7 in complex with AMP-PNP Deposited 2023-11-30 | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain B
1–346（346 aa）
|
Mutation：W132R,S164D, T170E | YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1M (NH4)3 citrate
15% PEG 3350
|
Resolution 1.94 Å R-free 0.340 |
| 8S0R Cryo-EM structure of CAK modified by covalent inhibitor SY-1365 Deposited 2024-02-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | A1H46 ~{N}-[(1~{S},3~{R})-3-[[5-chloranyl-4-(1~{H}-indol-3-yl)pyrimidin-2-yl]amino]-1-methyl-cyclohexyl]-5-[4-(dimethylamino)butanoylamino]pyridine-2-carboxamide × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 8S0T Cryo-EM structure of CAK in complex with SY-5609 Deposited 2024-02-14 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | YNK 7-dimethylphosphoryl-3-[2-[[(3~{S})-6,6-dimethylpiperidin-3-yl]amino]-5-(trifluoromethyl)pyrimidin-4-yl]-1~{H}-indole-6-carbonitrile × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9；Buffer contained 54 uM inhibitor SY-5609.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9HIX Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with THZ1 Deposited 2024-11-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | V0G N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)-4-{[4-(dimethylamino)butanoyl]amino}benzamide × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9HIY Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with ATPgS Deposited 2024-11-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9HJ0 Cryo-EM structure of CAK (CDK7 D97N mutant) in complex with Samuraciclib Deposited 2024-11-27 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | I74 (3R,4R)-4-[[[7-[(phenylmethyl)amino]-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-5-yl]amino]methyl]piperidin-3-ol × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9I9I Cryo-EM structure of CAK-CDK11 Deposited 2025-02-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9I9J Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-nitrate) Deposited 2025-02-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9I9K Cryo-EM structure of CAK-CDK2 (determined in the presence of ADP-AlFx) Deposited 2025-02-06 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 4 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 9QCV Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP Deposited 2025-03-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9QCX Cryo-EM structure of apo-CAK-CDK2-cyclin A2 Deposited 2025-03-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9QJN Cryo-EM structure of the human CAK bound to OTS964 Deposited 2025-03-19 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | NK3 OTS964 × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric（5） Consistent with protein count |
Chain J
1–346（346 aa）
|
Not recorded | ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |