1g3n

STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX

Method: X-RAY DIFFRACTION D_max: 119.7 Å Quality: GOOD

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

CYCLIN-DEPENDENT KINASE 6

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–326	Not recorded	CYCLIN-DEPENDENT KINASE 6 INHIBITOR × 1 （P42773） V-CYCLIN × 1 （O40946）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 1–326	Not recorded	CYCLIN-DEPENDENT KINASE 6 INHIBITOR × 1 （P42773） V-CYCLIN × 1 （O40946）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–326 Chain E； UniProt 1–326	Not recorded	V-CYCLIN × 2 （O40946）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–326 Chain E； UniProt 1–326	Not recorded	CYCLIN-DEPENDENT KINASE 6 INHIBITOR × 2 （P42773）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262

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 1G3N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BI7 MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURE OF THE CDK6-P16INK4A TUMOR SUPPRESSOR COMPLEX Deposited 1998-06-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.330
1BI8 MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX Deposited 1998-06-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–326（326 aa） Chain C 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.308
1BLX P19INK4D/CDK6 COMPLEX Deposited 1998-07-21	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 1–326（326 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.90 Å R-free 0.253
1JOW Crystal structure of a complex of human CDK6 and a viral cyclin Deposited 2001-07-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–308（308 aa） Fragment：residues 1-308	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris/HCL, sodium chloride, PEG 3350, calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 3.10 Å R-free 0.323
1XO2 Crystal structure of a human cyclin-dependent kinase 6 complex with a flavonol inhibitor, fisetin Deposited 2004-10-05	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 1–308（308 aa）	Not recorded	FSE 3,7,3',4'-TETRAHYDROXYFLAVONE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.90 Å R-free 0.313
2EUF X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991 Deposited 2005-10-28	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 1–308（308 aa） Fragment：fragment 1-308	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1 LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；50 mM Tris/HCl pH 8.0, 0.1 M CaAcetate, 10% PEG3350, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.00 Å R-free 0.306
2F2C X-ray structure of human CDK6-Vcyclinwith the inhibitor aminopurvalanol Deposited 2005-11-16	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 1–308（308 aa） Fragment：fragment 1-308	Not recorded	SO4 SULFATE ION × 1 AP9 (2S)-2-({6-[(3-AMINO-5-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；50 mM Tris/HCl pH 8.0, 0.1 M CaOAc, 13% PEG 3350, 10 mM DTT, 0.1M sulfobetaine, 1mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.301
3NUP CDK6 (monomeric) in complex with inhibitor Deposited 2010-07-07	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	3NU 4-[3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(1-methylpiperidin-4-yl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；298 K；0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3, EVAPORATION, temperature 298K	Resolution 2.60 Å R-free 0.264
3NUX CDK6 (monomeric) in complex with inhibitor Deposited 2010-07-07	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	3NV 4-[5-chloro-3-(1-methylethyl)-1H-pyrazol-4-yl]-N-(5-piperazin-1-ylpyridin-2-yl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES pH 6.0, 12% PEG3350, 0.1M NH4NO3 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.266
4AUA Liganded X-ray crystal structure of cyclin dependent kinase 6 (CDK6) Deposited 2012-05-15	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 1–301（301 aa） Fragment：KINASE DOMAIN, RESIDUES 1-301	Not recorded	4AU 1H-benzimidazol-2-yl(1H-pyrrol-2-yl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.7；287 K；5MG/ML 0.1 M MES/NAOH PH 5.7,, 4.5% W/V PEG 3350, 25 MM SODIUM NITRATE, 10% V/V GLYCEROL, 10 DEGREES CELSIUS	Resolution 2.31 Å R-free 0.277
4EZ5 CDK6 (monomeric) in complex with inhibitor Deposited 2012-05-02	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	0RS {5-[4-(dimethylamino)piperidin-1-yl]-1H-imidazo[4,5-b]pyridin-2-yl}[2-(isoquinolin-4-yl)pyridin-4-yl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.1M MES pH 6.0, 12% PEG-3350, 0.1M NH4NO3, EVAPORATION, temperature 298K, VAPOR DIFFUSION, HANGING DROP	Resolution 2.70 Å R-free 0.287
4TTH Crystal structure of a CDK6/Vcyclin complex with inhibitor bound Deposited 2014-06-20	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 1–326（326 aa）	Not recorded	24V 9-cyclopentyl-N-(5-piperazin-1-ylpyridin-2-yl)pyrido[4,5]pyrrolo[1,2-d]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10 mM TRIS pH 7.9, 100 mM calcium acetate, 10 mM DTT, 8-12% PEG 3350, 100 mM NDSB-201	Resolution 2.90 Å R-free 0.337
5L2I The X-ray co-crystal structure of human CDK6 and Palbociclib. Deposited 2016-08-01	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	LQQ 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350.	Resolution 2.75 Å R-free 0.304
5L2S The X-ray co-crystal structure of human CDK6 and Abemaciclib. Deposited 2016-08-02	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	6ZV N-{5-[(4-ethylpiperazin-1-yl)methyl]pyridin-2-yl}-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-benzimidazol-6-yl]py rimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350	Resolution 2.27 Å R-free 0.249
5L2T The X-ray co-crystal structure of human CDK6 and Ribociclib. Deposited 2016-08-02	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 1–301（301 aa） Fragment：UNP residues 1-301	Not recorded	6ZZ 7-cyclopentyl-N,N-dimethyl-2-{[5-(piperazin-1-yl)pyridin-2-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；1:1 (protein to well buffer) with well buffer containing: 0.1 M MES pH 6.0, 70 - 80 mM NH4NO3, 10 - 15% polyethyleneglycol 3350	Resolution 2.37 Å R-free 0.258
6OQL CDK6 in complex with Cpd13 (R)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine Deposited 2019-04-26	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 11–301（291 aa） Fragment：kinase domain	Not recorded	N1A 5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；292 K；13-17% PEG 3350, 80 mM NH4NO3, 100 mM MES pH 6.0	Resolution 2.71 Å R-free 0.253
6OQO CDK6 in complex with Cpd24 N-(5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)pyrimidin-2-amine Deposited 2019-04-26	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 11–301（291 aa） Fragment：kinase domain	Not recorded	N1J N-[5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl]-5-fluoro-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；292 K；17 % w/v PEG 3,350, 100 mM HEPES, pH 7.5, 200 mM NaCl, 20 mM L-Glutathione	Resolution 1.98 Å R-free 0.264
8I0M Structure of CDK6 in complex with inhibitor Deposited 2023-01-11	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 1–301（301 aa）	Not recorded	NJ6 2-[(4-azanylcyclohexyl)amino]-7-cyclopentyl-~{N},~{N}-dimethyl-pyrrolo[2,3-d]pyrimidine-6-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M BIS-TRIS pH 7.0, 20% PEG 4,000	Resolution 2.78 Å R-free 0.282
9D8U Crystal structure of CDK6 in complex with atirmociclib Deposited 2024-08-20	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 1–301（301 aa）	Not recorded	A1AZ4 Atirmociclib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；286.15 K；Well Ingredients: Salt: 0.133 M Ammonium Nitrate Precipitant: 5.09 %w/v PEG 3350 Buffer: 0.1 M MES (pH 6.00) Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 0.3 uL Drop protein volume: 0.3 uL	Resolution 2.00 Å R-free 0.253
9PE7 CDK6 to CDK4 active site surrogate in complex with compound 6 Deposited 2025-07-01	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 1–301（301 aa）	Mutation：E21V, K26T, T106R, Q149E	A1CIF (3R,4R)-4-({(4M)-5-fluoro-4-[4-fluoro-2-methyl-1-(propan-2-yl)-1H-1,3-benzimidazol-6-yl]pyrimidin-2-yl}amino)-1-(methanesulfonyl)piperidin-3-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 100.0 uL Well Ingredients: Precipitant: 4.0 %w/v (8.0 uL of stock 50.0 %w/v) PEG 3350 Salt: 5.0 mM (5.0 uL of stock 100.0 mM) Calcium chloride dihydrate Salt: 0.0928571429 M (9.2857142857 uL of stock 1.0 M) Ammonium Nitrate Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 1.0 uL Drop protein volume: 1.0 uL Protein formulation name: LJIC-3730A1 + PF-6825089 b Protein Formulation Composition: Protein: CDK6 mutated to look like CDK4 (6.87 mg/mL) Compound: PF-6825089 (1.00 mM)	Resolution 2.05 Å R-free 0.267
9PE8 CDK6 to CDK4 active site surrogate in complex with PF-07220060 Deposited 2025-07-01	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 1–301（301 aa）	Mutation：E21V, K26T, T106R, Q149E	A1AZ4 Atirmociclib × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；286.15 K；Well volume: 50.0 uL Well Ingredients: Salt: 0.2714285714 M (1.357142857 uL of stock 10.0 M) Ammonium Nitrate Precipitant: 9.4545454545 %w/v (9.4545454545 uL of stock 50.0 %w/v) PEG 3350 Buffer: 0.1 M (5.0 uL of stock 1.0 M) MES (pH 6.00) Plate setup temperature: 21 C Plate incubation temperature: 13 C Drop volume from well: 0.3 uL Drop protein volume: 0.3 uL Protein Formulation Composition: Protein: quad mutant (6.80 mg/mL) (0.20 mM) Ligand: PF-7220060 (1.00 mM)	Resolution 1.80 Å R-free 0.252

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 1–326 Author chain E； PDBConstruct 1–326； UniProt 1–326

CYCLIN-DEPENDENT KINASE 6 INHIBITOR

Homo sapiens

UniProt P42773

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 1–168	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 1 （Q00534） V-CYCLIN × 1 （O40946）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–168	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 1 （Q00534） V-CYCLIN × 1 （O40946）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–168 Chain F； UniProt 1–168	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 2 （Q00534）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1G3N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BU9 SOLUTION STRUCTURE OF P18-INK4C, 21 STRUCTURES Deposited 1998-09-15	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–168（168 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K	Resolution not provided
1IHB CRYSTAL STRUCTURE OF P18-INK4C(INK6) Deposited 1997-10-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–162（162 aa） Chain B 1–162（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；VAPOR DIFFUSION, 4 DEG. C, 2 MICROLITER HANGING DROP CONTAINING 5 MG/ML PROTEIN, 20 MM TRIS (PH 8.5), 25 MM (NH4)2 HPO4, 0.5 MM DDT, 7% PEG 6K, 1 MM NACL EQUILIBRATED OVER A RESERVOIR CONTAINING 14% PEG 6K AND 2 M NACL. WITHIN 8 DAYS, 0.2 X 0.2 X 0.4 MM CRYSTALS., vapor diffusion - hanging drop	Resolution 1.95 Å R-free 0.289
1MX2 Structure of F71N mutant of p18INK4c Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–168（168 aa）	Mutation：F71N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；20 mM Tris, 25mM (NH4)2HPO4, 0.5 mM DTT, 7% PEG 6000, 2 M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.25 Å R-free 0.254
1MX2 Structure of F71N mutant of p18INK4c Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–168（168 aa）	Mutation：F71N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；20 mM Tris, 25mM (NH4)2HPO4, 0.5 mM DTT, 7% PEG 6000, 2 M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.25 Å R-free 0.254
1MX4 Structure of p18INK4c (F82Q) Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–168（168 aa）	Mutation：F82Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；5 mg/ml protein, 20 mM Tris (pH 8.5), 0.5 mM DTT, 14 % PEG 6000, 2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.260
1MX4 Structure of p18INK4c (F82Q) Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–168（168 aa）	Mutation：F82Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；5 mg/ml protein, 20 mM Tris (pH 8.5), 0.5 mM DTT, 14 % PEG 6000, 2 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.260
1MX6 Structure of p18INK4c (F92N) Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–168（168 aa）	Mutation：F92N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；5 mg/ml protein, 20 mM Tris (pH 8.5), 0.5 mM DTT, 14 % PEG 6000 and 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.263
1MX6 Structure of p18INK4c (F92N) Deposited 2002-10-01	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–168（168 aa）	Mutation：F92N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；273 K；5 mg/ml protein, 20 mM Tris (pH 8.5), 0.5 mM DTT, 14 % PEG 6000 and 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.00 Å R-free 0.263

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDN2C_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–168； UniProt 1–168 Author chain F； PDBConstruct 1–168； UniProt 1–168

V-CYCLIN

Human herpesvirus 8

UniProt O40946

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 1–257	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 1 （Q00534） CYCLIN-DEPENDENT KINASE 6 INHIBITOR × 1 （P42773）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 1–257	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 1 （Q00534） CYCLIN-DEPENDENT KINASE 6 INHIBITOR × 1 （P42773）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–257 Chain G； UniProt 1–257	Not recorded	CYCLIN-DEPENDENT KINASE 6 × 2 （Q00534）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；(NH4)2SO4, Dioxane, Tris-HCl, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.262

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	O40946_HHV8
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–257； UniProt 1–257 Author chain G； PDBConstruct 1–257； UniProt 1–257

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1g3n
Deposition date deposition_date	2000-10-24
Structure title title	STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX
Keywords keywords	Cyclin-dependent kinase, INK4 inhibitor, Viral cyclin, cell cycle, signaling protein; cell cycle, signaling protein
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	37.11 Å
Radius of gyration Rg (electron density) rg_electron	36.16 Å
Forward intensity I(0) i0	339182000.00
Molecular weight molecular_weight	151130.0 kDa
Excluded volume excluded_volume	190370 Å³
Envelope volume envelope_volume	249840 Å³
Hydration-shell volume shell_volume	57446 Å³
Envelope diameter envelope_diameter	130.5 Å
Shell Rg shell_rg	42.84 Å
Envelope Rg envelope_rg	35.33 Å
Shape Rg shape_rg	36.16 Å
Total Rg total_rg	36.64 Å
Total atoms total_atoms	10644
Residues n_residues	1362
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	119.7 Å
Rg (real space) rg_real	36.99 Å
Rg uncertainty (real space) rg_real_error	0.89 Å
I(0) (real space) i0_real	3.3920e+08
I(0) uncertainty (real space) i0_real_error	6.3620e+06
Rg (reciprocal space) rg_reciprocal	37.06 Å
I(0) (reciprocal space) i0_reciprocal	339200000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.3 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.306
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55580000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CYCLIN-DEPENDENT KINASE 6
Molecular weight formula_weight	36987.3 kDa
EC 编号 ec_number	2.7.1.37
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	10644

MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLDFLHSHRVVHRDLKPQNILVTSSGQIKLADFGLARIYSFQMALTSVVVTLWYRAPEVLLQSSYATPVDLWSVGCIFAEMFRRKPLFRGSSDVDQLGKILDVIGLPGEEDWPRDVALPRQAFHSKSAQPIEKFVTDIDELGKDLLLKCLTFNPAKRISAYSALSHPYFQDLERCKENLDSHLPPSQNTSELNTA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	unidentified baculovirus

Entity 2 Entity 2 polymer

Description description	CYCLIN-DEPENDENT KINASE 6 INHIBITOR
Molecular weight formula_weight	18149.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F

MAEPWGNELASAAARGDLEQLTSLLQNNVNVNAQNGFGRTALQVMKLGNPEIARRLLLRGANPDLKDRTGFAVIHDAARAGFLDTLQTLLEFQADVNIEDNEGNLPLHLAAKEGHLRVVEFLVKHTASNVGHRNHKGDTACDLARLYGRNEVVSLMQANGAGGATNLQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	V-CYCLIN
Molecular weight formula_weight	28094.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G

MATANNPPSGLLDPTLCEDRIFYNILEIEPRFLTSDSVFGTFQQSLTSHMRKLLGTWMFSVCQEYNLEPNVVALALNLLDRLLLIKQVSKEHFQKTGSACLLVASKLRSLTPISTSSLCYAAADSFSRQELIDQEKELLEKLAWRTEAVLATDVTSFLLLKLVGGSQHLDFWHHEVNTLITKALVDPLTGSLPASIISAAGCALLVPANVIPQDTHSGGVVPQLASILGCDVSVLQAAVEQILTSVSDFDLRILDSY

来源 Source

来源生物 organism	Human herpesvirus 8
NCBI Class编号 ncbi_taxonomy_id	37296
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1g3na_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d1g3nb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

Domain ID domain_id	d1g3nc1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d1g3nc2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d1g3ne_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d1g3nf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

Domain ID domain_id	d1g3ng1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d1g3ng2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

CATH v4.4 (10 domains)

Domain ID domain_id	1g3nA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1g3nA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	1g3nB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	1g3nC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	1g3nC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	1g3nE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1g3nE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	1g3nF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	1g3nG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	1g3nG02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

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8. Citations (1)

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Unit-cell length a length_a	77.780 Å
Unit-cell length b length_b	146.950 Å
Unit-cell length c length_c	164.820 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2280
R_work r_work	0.2240
R_free r_free	0.2620

fit	/app/data/saxs_computation/g3/1g3n/1g3n.fit
pddf	/app/data/pr_computation/g3/1g3n/1g3n.pr.out
profile	/app/data/saxs_computation/g3/1g3n/1g3n.dat

STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX

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

CYCLIN-DEPENDENT KINASE 6

State in the Current Structure

Other States of the Same Protein in the Database

CYCLIN-DEPENDENT KINASE 6 INHIBITOR

State in the Current Structure

Other States of the Same Protein in the Database

V-CYCLIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)