← Back to search
6gu2

CDK1/CyclinB/Cks2 in complex with Flavopiridol

Method: X-RAY DIFFRACTION Dmax: 91.8 Å Quality: EXCELLENT
▼

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

Cyclin-dependent kinase 1

Homo sapiens

UniProt P06493

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–297 Not recorded G2/mitotic-specific cyclin-B1 × 1 （P14635） Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552） F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor Resolution 2.00 Å R-free 0.239

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 6GU2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC
Chain A 1–297（297 aa）
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–297（297 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.70 Å R-free 0.260
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–297（297 aa） Fragment：Fall Armyworm
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K
Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–297（297 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–297（297 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–297（297 aa）
Not recorded FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–297（297 aa）
Not recorded FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.73 Å R-free 0.253
6GU6 CDK1/Cks2 in complex with Dinaciclib Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–297（297 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR
Resolution 2.33 Å R-free 0.246
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–297（297 aa）
Not recorded FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–297（297 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6TWN Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223) Deposited 2020-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 207–223（17 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M Na citrate pH 5.6, 20% Isopropanol and 20% PEG4K
Resolution 2.28 Å R-free 0.262
6TWN Crystal structure of Talin1 R7R8 in complex with CDK1 (206-223) Deposited 2020-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 207–223（17 aa）
Not recorded GOL GLYCEROL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.1M Na citrate pH 5.6, 20% Isopropanol and 20% PEG4K
Resolution 2.28 Å R-free 0.262
7NJ0 CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex Deposited 2021-02-14 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–297（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–297（297 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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

12 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDK1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–302； UniProt 1–297

G2/mitotic-specific cyclin-B1

Homo sapiens

UniProt P14635

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 165–433 Not recorded Cyclin-dependent kinase 1 × 1 （P06493） Cyclin-dependent kinases regulatory subunit 2 × 1 （P33552） F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor Resolution 2.00 Å R-free 0.239

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 6GU2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2B9R Crystal Structure of Human Cyclin B1 Deposited 2005-10-12 Different construct Different mutation/modification 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 165–433（269 aa） Fragment：Residues 165-433
Mutation：C167S, C283S, C350S, E183A, E184A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.90 Å R-free 0.308
2B9R Crystal Structure of Human Cyclin B1 Deposited 2005-10-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 165–433（269 aa） Fragment：Residues 165-433
Mutation：C167S, C283S, C350S, E183A, E184A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.90 Å R-free 0.308
2JGZ Crystal structure of phospho-CDK2 in complex with Cyclin B Deposited 2007-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 167–426（260 aa） Fragment：RESIDUES 167-426
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.9-1.2 M AMMONIUM SULPHATE, 100 MM MES PH 6.0-6.5, 100 MM POTASSIUM CHLORIDE
Resolution 2.90 Å R-free 0.275
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC
Chain B 165–433（269 aa）
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 165–433（269 aa） Fragment：UNP residues 165-433
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.70 Å R-free 0.260
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 165–433（269 aa）
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K
Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 165–433（269 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 165–433（269 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 165–433（269 aa）
Not recorded FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 165–433（269 aa）
Not recorded FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.73 Å R-free 0.253
7NJ0 CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex Deposited 2021-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–433（433 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8TAR APC/C-CDH1-UBE2C-Ubiquitin-CyclinB-NTD Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain B 39–50（12 aa） Fragment：NTD (residues 39-50)
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8TAU APC/C-CDH1-UBE2C-UBE2S-Ubiquitin-CyclinB Deposited 2023-06-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric
Chain B 39–50（12 aa） Fragment：NTD (residues 39-50)
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9FH9 Structure of CyclinB1 N-terminus bound to the NCP Deposited 2024-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain K 1–21（21 aa）
Chain L 1–21（21 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9SKQ Cryo-EM structure of CAK-CDK1-cyclin B1 Deposited 2025-09-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–433（433 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

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCNB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–273； UniProt 165–433

Cyclin-dependent kinases regulatory subunit 2

Homo sapiens

UniProt P33552

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 1–79 Not recorded Cyclin-dependent kinase 1 × 1 （P06493） G2/mitotic-specific cyclin-B1 × 1 （P14635） F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor Resolution 2.00 Å R-free 0.239

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 6GU2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CKS HUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY IN CELL CYCLE CONTROL Deposited 1993-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 1–79（79 aa）
Chain B 1–79（79 aa）
Chain C 1–79（79 aa）
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC
Chain C 1–79（79 aa） Fragment：residues 165-433
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–79（79 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml
Resolution 2.70 Å R-free 0.260
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–79（79 aa）
Not recorded LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K
Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–79（79 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–79（79 aa）
Not recorded 4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Resolution 2.06 Å R-free 0.254
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–79（79 aa）
Not recorded FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–79（79 aa）
Not recorded FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor
Resolution 2.73 Å R-free 0.253
6GU6 CDK1/Cks2 in complex with Dinaciclib Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–79（79 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 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR
Resolution 2.33 Å R-free 0.246
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–79（79 aa）
Not recorded FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR
Resolution 2.75 Å R-free 0.274

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CKS2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 6–84； UniProt 1–79

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6gu2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6gu2
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6gu2
Deposition date deposition_date2018-06-19
Structure title titleCDK1/CyclinB/Cks2 in complex with Flavopiridol
Keywords keywordsCDK1, CYCLINB1, CKS2, INHIBITOR, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier29.61 Å
Radius of gyration Rg (electron density) rg_electron28.74 Å
Forward intensity I(0) i080608200.00
Molecular weight molecular_weight73398.0 kDa
Excluded volume excluded_volume93122 ų
Envelope volume envelope_volume114870 ų
Hydration-shell volume shell_volume33676 ų
Envelope diameter envelope_diameter101.1 Å
Shell Rg shell_rg35.75 Å
Envelope Rg envelope_rg28.53 Å
Shape Rg shape_rg28.74 Å
Total Rg total_rg29.47 Å
Total atoms total_atoms5170
Residues n_residues631
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax91.8 Å
Rg (real space) rg_real29.56 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real8.0610e+07
I(0) uncertainty (real space) i0_real_error1.1170e+06
Rg (reciprocal space) rg_reciprocal29.58 Å
I(0) (reciprocal space) i0_reciprocal80610000.0000
Solution quality estimate total_estimate0.9066
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.3 Å
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.592
Angular range angular_range— – 0.2700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25710000.0000
Real-space data points n_real_points55
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.963; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.893
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6gu2a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd6gu2a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd6gu2c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamilyd.97.1 — Cell cycle regulatory proteins
Family Family familyd.97.1.1 — Cell cycle regulatory proteins

CATH v4.4 (5 domains)

Domain ID domain_id6gu2A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id6gu2A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id6gu2B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id6gu2B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id6gu2C00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily10 — Cyclin-dependent kinase, regulatory subunit
▶

8. Citations (1)

▶

9. Files and Curves (10)