SAXSdb — 3o0g

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

Cell division protein kinase 5

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–292	Not recorded	Cyclin-dependent kinase 5 activator 1 × 1 （Q15078）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–292	Not recorded	Cyclin-dependent kinase 5 activator 1 × 1 （Q15078） 3O0 {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256

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 3O0G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Mutation：YES	RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–292（292 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	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 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 3 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	Different construct 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 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 3 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
4AU8 Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule Deposited 2012-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa） Fragment：RESIDUES 2-292 Chain B 2–292（291 aa） Fragment：RESIDUES 2-292	Not recorded	SO4 SULFATE ION × 6 Z3R 4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide × 2 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.4；pH 5.4	Resolution 1.90 Å R-free 0.234
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1 EDO 1,2-ETHANEDIOL × 10 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	64V 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	64V 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–292（291 aa）	Not recorded	61U 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile × 1 GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–292（291 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272

9 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–292； UniProt 1–292 Author chain B； PDBConstruct 1–292； UniProt 1–292

Cyclin-dependent kinase 5 activator 1

Homo sapiens

UniProt Q15078

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 145–293	Fragment：UNP residues 146-293	Cell division protein kinase 5 × 1 （Q00535）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 145–293	Fragment：UNP residues 146-293	Cell division protein kinase 5 × 1 （Q00535） 3O0 {4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；293 K；PEG 3350, KI, Bis-Tris Propane, pH 7, vapor diffusion, temperature 293K	Resolution 1.95 Å R-free 0.256

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 3O0G	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 147–293（147 aa） Fragment：RESIDUES 147-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1H4L Structure and regulation of the CDK5-p25(nck5a) complex Deposited 2001-05-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 147–293（147 aa） Fragment：RESIDUES 147-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；MICROSEEDING - PEG3350, 100 MM TRIS PH 7.6, 200 MM KI, 10 MM DTT, PROTEIN CONC.:7 MG/ML HANGING DROP 2+2 UL. TEMPERATURE 293K.	Resolution 2.65 Å R-free 0.287
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNG Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	ALH 6-PHENYL[5H]PYRROLO[2,3-B]PYRAZINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1M KI, 0.1M BISTRISPROPANE PH 7.0, 10MM DTT	Resolution 2.30 Å R-free 0.225
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNH Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Not recorded	IXM (Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.35 Å R-free 0.230
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa） Fragment：RESIDUES 100-307	Mutation：YES	RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
1UNL Structural mechanism for the inhibition of CD5-p25 from the roscovitine, aloisine and indirubin. Deposited 2003-09-10	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 100–307（208 aa） Fragment：RESIDUES 100-307	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；13% PEG 3350, 0.1 M KI, 0.1 M BISTRISPROPANE PH 7.0, 10 MM DTT	Resolution 2.20 Å R-free 0.219
6LDP Structure of CDK5R1-bound FEM1C Deposited 2019-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris-Hcl pH 7.9	Resolution 2.35 Å R-free 0.258
6LDP Structure of CDK5R1-bound FEM1C Deposited 2019-11-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris-Hcl pH 7.9	Resolution 2.35 Å R-free 0.258
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7CNG Structure of CDK5R1 bound FEM1B Deposited 2020-07-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 298–307（10 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.6M Magnesium sulfate hydrate, 0.1M BIS-TRIS propane pH 6.7	Resolution 3.49 Å R-free 0.267
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1 EDO 1,2-ETHANEDIOL × 10 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
7VDP The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	65L [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.09 Å R-free 0.229
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	64V 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDQ The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	64V 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.91 Å R-free 0.284
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDR The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	63I (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1,6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 2.55 Å R-free 0.256
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 100–307（208 aa）	Not recorded	61U 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile × 1 GOL GLYCEROL × 8 EDO 1,2-ETHANEDIOL × 17 CL CHLORIDE ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272
7VDS The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 Deposited 2021-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 100–307（208 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1M MES pH 5.5, 0.3M MgCl2, 20% PEG3350	Resolution 3.05 Å R-free 0.272

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

View Construct and Data Evidence

UniProt name	CD5R1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–149； UniProt 145–293 Author chain E； PDBConstruct 1–149； UniProt 145–293

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3o0g
Deposition date deposition_date	2010-07-19
Structure title title	Crystal Structure of Cdk5:p25 in complex with an ATP analogue
Keywords keywords	kinase, Kinase activator complex, kinase inhibitor complex, TRANSFERASE-TRANSFERASE ACTIVATOR complex; TRANSFERASE/TRANSFERASE ACTIVATOR
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	45.08 Å
Radius of gyration Rg (electron density) rg_electron	45.04 Å
Forward intensity I(0) i0	132693000.00
Molecular weight molecular_weight	97683.0 kDa
Excluded volume excluded_volume	123410 Å³
Envelope volume envelope_volume	173720 Å³
Hydration-shell volume shell_volume	32445 Å³
Envelope diameter envelope_diameter	146.7 Å
Shell Rg shell_rg	49.55 Å
Envelope Rg envelope_rg	43.44 Å
Shape Rg shape_rg	45.04 Å
Total Rg total_rg	45.25 Å
Total atoms total_atoms	6871
Residues n_residues	851
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	135.2 Å
Rg (real space) rg_real	45.47 Å
Rg uncertainty (real space) rg_real_error	1.51 Å
I(0) (real space) i0_real	1.3270e+08
I(0) uncertainty (real space) i0_real_error	2.6010e+06
Rg (reciprocal space) rg_reciprocal	45.08 Å
I(0) (reciprocal space) i0_reciprocal	132600000.0000
Solution quality estimate total_estimate	0.4696
Solution quality rating solution_quality	SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	27.0 Å
Skewness Skewness skewness	0.275
Kurtosis Kurtosis kurtosis	-1.009
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9065000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.552; Stabil: 0.999; Sysdev: 0.010; Positv: 1.000; Valcen: 0.407; Smooth: 0.010

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cell division protein kinase 5
Molecular weight formula_weight	33349.5 kDa
EC 编号 ec_number	2.7.11.22
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7105

MQKYEKLEKIGEGTYGTVFKAKNRETHEIVALKRVRLDDDDEGVPSSALREICLLKELKHKNIVRLHDVLHSDKKLTLVFEFCDQDLKKYFDSCNGDLDPEIVKSFLFQLLKGLGFCHSRNVLHRDLKPQNLLINRNGELKLANFGLARAFGIPVRCYSAEVVTLWYRPPDVLFGAKLYSTSIDMWSAGCIFAELANAGRPLFPGNDVDDQLKRIFRLLGTPTEEQWPSMTKLPDYKPYPMYPATTSLVNVVPKLNATGRDLLQNLLKCNPVQRISAEEALQHPYFSDFCPP

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinase 5 activator 1
Molecular weight formula_weight	17216.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E

QASTSELLRCLGEFLCRRCYRLKHLSPTDPVLWLRSVDRSLLLQGWQDQGFITPANVVFLYMLCRDVISSEVGSDHELQAVLLTCLYLSYSYMGNEISYPLKPFLVESCKEAFWDRCLSVINLMSSKMLQINADPHYFTQVFSDLKNES

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	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	{4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone
Molecular weight formula_weight	374.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	234

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3o0ga_
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	d3o0gb_
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	d3o0gd_
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	d3o0ge_
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 (6 domains)

Domain ID domain_id	3o0gA01
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	3o0gA02
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	3o0gB01
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	3o0gB02
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	3o0gD00
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	3o0gE00
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	117.124 Å
Unit-cell length b length_b	117.124 Å
Unit-cell length c length_c	155.599 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2276
R_work r_work	0.2261
R_free r_free	0.2563

fit	/app/data/saxs_computation/o0/3o0g/3o0g.fit
pddf	/app/data/pr_computation/o0/3o0g/3o0g.pr.out
profile	/app/data/saxs_computation/o0/3o0g/3o0g.dat

Crystal Structure of Cdk5:p25 in complex with an ATP analogue

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

Cell division protein kinase 5

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-dependent kinase 5 activator 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)