SAXSdb — 1cks

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

CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–79 Chain B； UniProt 1–79 Chain C； UniProt 1–79	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.10 Å

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 1CKS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Y72 Human CDK1/CyclinB1/CKS2 With Inhibitor Deposited 2015-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: TRIMERIC	Chain C 1–79（79 aa） Fragment：residues 165-433	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；Conditions around 0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.30 Å R-free 0.252
4YC3 CDK1/CyclinB1/CKS2 Apo Deposited 2015-02-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.7；277 K；0.1M MES/imidazole buffer (pH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K Protein at 10-12 mg/ml	Resolution 2.70 Å R-free 0.260
5HQ0 Ternary complex of human proteins CDK1, Cyclin B and CKS2, bound to an inhibitor Deposited 2016-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	LZ9 {[(2,6-difluorophenyl)carbonyl]amino}-N-(4-fluorophenyl)-1H-pyrazole-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1 M MES pH6.7, 6.55 MPD, 5% PEG4K, 10% PEG 1K	Resolution 2.30 Å R-free 0.252
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
5LQF CDK1/CyclinB1/CKS2 in complex with NU6102 Deposited 2016-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–79（79 aa）	Not recorded	4SP O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML	Resolution 2.06 Å R-free 0.254
6GU2 CDK1/CyclinB/Cks2 in complex with Flavopiridol Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	F9Z 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.00 Å R-free 0.239
6GU3 CDK1/CyclinB/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.65 Å R-free 0.258
6GU4 CDK1/CyclinB/Cks2 in complex with CGP74514A Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–79（79 aa）	Not recorded	FC8 ~{N}2-[(1~{R},2~{S})-2-azanylcyclohexyl]-~{N}6-(3-chlorophenyl)-9-ethyl-purine-2,6-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M MES/IMIDAZOLE BUFFER (PH6.7), 6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML + 0.5mM Inhibitor	Resolution 2.73 Å R-free 0.253
6GU6 CDK1/Cks2 in complex with Dinaciclib Deposited 2018-06-19	Different 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 1–79（79 aa）	Not recorded	1QK 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M BIS-TRIS(PH6.5), 0.2M SODIUM NITRATE 20% PEG3350, PROTEIN AT 10-12 MG/ML, 0.5Mm INHIBITOR	Resolution 2.33 Å R-free 0.246
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different 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 1–79（79 aa）	Not recorded	FB8 4-(2-methyl-3-propan-2-yl-imidazol-4-yl)-~{N}-(4-methylsulfonylphenyl)pyrimidin-2-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–79（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–79（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274
6GU7 CDK1/Cks2 in complex with AZD5438 Deposited 2018-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–79（79 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；CONDITIONS AROUND 0.1M TRIS/BICINE (PH8.5), 10% PEG8K, 20% ETHYLENE GLYCOL PROTEIN AT 10-12 MG/ML, 0.5mM INHIBITOR	Resolution 2.75 Å R-free 0.274

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

View Construct and Data Evidence

UniProt name	CKS2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 1–79 Author chain B； PDBConstruct 1–79； UniProt 1–79 Author chain C； PDBConstruct 1–79； UniProt 1–79

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cks
Deposition date deposition_date	1993-09-16
Structure title title	HUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY IN CELL CYCLE CONTROL
Keywords keywords	CELL DIVISION; CELL DIVISION
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	23.71 Å
Radius of gyration Rg (electron density) rg_electron	22.58 Å
Forward intensity I(0) i0	15406200.00
Molecular weight molecular_weight	28962.0 kDa
Excluded volume excluded_volume	36179 Å³
Envelope volume envelope_volume	59098 Å³
Hydration-shell volume shell_volume	22661 Å³
Envelope diameter envelope_diameter	71.5 Å
Shell Rg shell_rg	28.65 Å
Envelope Rg envelope_rg	21.99 Å
Shape Rg shape_rg	22.52 Å
Total Rg total_rg	23.70 Å
Total atoms total_atoms	2046
Residues n_residues	230
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	70.6 Å
Rg (real space) rg_real	23.54 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.5410e+07
I(0) uncertainty (real space) i0_real_error	1.9430e+05
Rg (reciprocal space) rg_reciprocal	23.59 Å
I(0) (reciprocal space) i0_reciprocal	15410000.0000
Solution quality estimate total_estimate	0.7434
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.3 Å
Skewness Skewness skewness	0.003
Kurtosis Kurtosis kurtosis	-0.659
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3140000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 0.286; Positv: 1.000; Valcen: 0.992; Smooth: 0.963

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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 SUBUNIT, TYPE 2
Molecular weight formula_weight	9879.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2270

MAHKQIYYSDKYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEWRRLGVQQSLGWVHYMIHEPEPHILLFRRPLPKDQQK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1cksa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

Domain ID domain_id	d1cksb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

Domain ID domain_id	d1cksc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.97 — Cell cycle regulatory proteins
Superfamily Superfamily superfamily	d.97.1 — Cell cycle regulatory proteins
Family Family family	d.97.1.1 — Cell cycle regulatory proteins

CATH v4.4 (3 domains)

Domain ID domain_id	1cksA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

Domain ID domain_id	1cksB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

Domain ID domain_id	1cksC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	170 — Cyclin-Dependent Kinase Subunit Type 2
Homologous superfamily homologous superfamily	10 — Cyclin-dependent kinase, regulatory subunit

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8. Citations (1)

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Unit-cell length a length_a	100.100 Å
Unit-cell length b length_b	57.600 Å
Unit-cell length c length_c	51.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	—

fit	/app/data/saxs_computation/ck/1cks/1cks.fit
pddf	/app/data/pr_computation/ck/1cks/1cks.pr.out
profile	/app/data/saxs_computation/ck/1cks/1cks.dat

HUMAN CKSHS2 ATOMIC STRUCTURE: A ROLE FOR ITS HEXAMERIC ASSEMBLY IN CELL CYCLE CONTROL

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

CYCLIN-DEPENDENT KINASE SUBUNIT, TYPE 2

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