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1bi8

MECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX

Method: X-RAY DIFFRACTION Dmax: 110.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLIN-DEPENDENT KINASE 6

Homo sapiens

UniProt Q00534

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–326 Chain C； UniProt 1–326 Not recorded CYCLIN-DEPENDENT KINASE INHIBITOR × 2 （P55273） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.308

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 1BI8 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 construct Different mutation/modification 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
1BLX P19INK4D/CDK6 COMPLEX Deposited 1998-07-21 Different construct Different mutation/modification 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
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–326（326 aa）
Not recorded No recorded non-water small molecule 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
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–326（326 aa）
Not recorded No recorded non-water small molecule 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
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–326（326 aa）
Chain E 1–326（326 aa）
Not recorded No recorded non-water small molecule 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
1G3N STRUCTURE OF A P18(INK4C)-CDK6-K-CYCLIN TERNARY COMPLEX Deposited 2000-10-24 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–326（326 aa）
Chain E 1–326（326 aa）
Not recorded No recorded non-water small molecule 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
1JOW Crystal structure of a complex of human CDK6 and a viral cyclin Deposited 2001-07-31 Different construct Different mutation/modification 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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 mutation/modification 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 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） 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 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） 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 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） 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 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） 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 construct Different mutation/modification 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 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） 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 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） 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 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） 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 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 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 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 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 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）
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 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）
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 24 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 C； PDBConstruct 1–326； UniProt 1–326

CYCLIN-DEPENDENT KINASE INHIBITOR

Homo sapiens

UniProt P55273

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–166 Chain D； UniProt 1–166 Not recorded CYCLIN-DEPENDENT KINASE 6 × 2 （Q00534） X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.80 Å R-free 0.308

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 1BI8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BD8 STRUCTURE OF CDK INHIBITOR P19INK4D Deposited 1998-05-12 Different construct 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 7–162（156 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；PROTEIN WAS CRYSTALLIZED FROM 35% PEG 4000, 200 MM MGSO4 AND 200 MM TRIS/HCL PH 8.5, SITTING DROP METHOD, AT 4 DEG. C., vapor diffusion - sitting drop, temperature 277K
Resolution 1.80 Å R-free 0.260

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDN2D_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–166； UniProt 1–166 Author chain D； PDBConstruct 1–166； UniProt 1–166

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 1bi8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bi8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bi8
Deposition date deposition_date1998-06-22
Structure title titleMECHANISM OF G1 CYCLIN DEPENDENT KINASE INHIBITION FROM THE STRUCTURES CDK6-P19INK4D INHIBITOR COMPLEX
Keywords keywords;CYCLIN DEPENDENT KINASE, CYCLIN DEPENDENT KINASE INHIBITORY PROTEIN, CDK, INK4, CELL CYCLE, COMPLEX (KINASE-INHIBITOR), COMPLEX (KINASE-INHIBITOR) complex ;; COMPLEX (KINASE/INHIBITOR)
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.82 Å
Radius of gyration Rg (electron density) rg_electron35.20 Å
Forward intensity I(0) i0129852000.00
Molecular weight molecular_weight92711.0 kDa
Excluded volume excluded_volume116640 ų
Envelope volume envelope_volume154190 ų
Hydration-shell volume shell_volume36471 ų
Envelope diameter envelope_diameter104.9 Å
Shell Rg shell_rg42.11 Å
Envelope Rg envelope_rg34.05 Å
Shape Rg shape_rg35.20 Å
Total Rg total_rg35.71 Å
Total atoms total_atoms6538
Residues n_residues838
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.0 Å
Rg (real space) rg_real35.74 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real1.2990e+08
I(0) uncertainty (real space) i0_real_error2.0490e+06
Rg (reciprocal space) rg_reciprocal35.80 Å
I(0) (reciprocal space) i0_reciprocal129900000.0000
Solution quality estimate total_estimate0.9035
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.073
Kurtosis Kurtosis kurtosis-0.908
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19070000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.968
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1bi8a_
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_idd1bi8b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamilyd.211.1 — Ankyrin repeat
Family Family familyd.211.1.1 — Ankyrin repeat
Domain ID domain_idd1bi8c_
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_idd1bi8d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamilyd.211.1 — Ankyrin repeat
Family Family familyd.211.1.1 — Ankyrin repeat

CATH v4.4 (6 domains)

Domain ID domain_id1bi8A01
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_id1bi8A02
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_id1bi8B00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain
Domain ID domain_id1bi8C01
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_id1bi8C02
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_id1bi8D00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily20 — Ankyrin repeat-containing domain
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8. Citations (1)

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9. Files and Curves (10)