SAXSdb — 7tcy

▼

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

Non-receptor tyrosine-protein kinase TNK1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 589–666	Fragment：UBA domain (UNP residues 589-666) Mutation：P589G, C610A, C644A	FMT FORMIC ACID × 3 PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；100 mM Bis-Tris, pH 6.8, 100 mM magnesium formate	Resolution 1.54 Å R-free 0.214
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 589–666	Fragment：UBA domain (UNP residues 589-666) Mutation：P589G, C610A, C644A	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；100 mM Bis-Tris, pH 6.8, 100 mM magnesium formate	Resolution 1.54 Å R-free 0.214

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 7TCY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7T8J The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a GSGG linker Deposited 2021-12-16	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,V112E,C610A,C644A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；1.2 uL of 1 mg/mL protein in 50 mM Tris pH 8.8, 200 mM KCl combined with 1.2 uL of 100 mM Bis-tris-propane, 2.5 M Ammonium Nitrate	Resolution 1.89 Å R-free 0.235
7TDY The ubiquitin-associated domain of human thirty-eight negative kinase 1, flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at low protein concentration Deposited 2022-01-03	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,V112E,C610A,C644A	FMT FORMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；1.2 uL of 2 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 7.00, 250 mM Mg-Formate.	Resolution 1.53 Å R-free 0.217
7U4W The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at traditional protein concentration Deposited 2022-03-01	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,V112E,C610A,C644A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；1.2 uL of 15 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.50, 750 mM Mg-Formate	Resolution 2.10 Å R-free 0.276
7U4Z The ubiquitin-associated domain of human thirty-eight negative kinase-1 flexibly fused to the 1TEL crystallization chaperone via a 2-glycine linker and crystallized at very low protein concentration Deposited 2022-03-01	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,V112E,C610A,C644A	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.2 uL of 0.5 mg/mL protein combined with 1.2 uL of 100 mM Bis-Tris, pH 6.00, 630-750 mM Mg-Formate.	Resolution 2.03 Å R-free 0.232
9CPL The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 2TEL crystallization chaperone via a 2-glycine linker Deposited 2024-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 590–666（77 aa）	Mutation：First TELSAM:R80S,V112E,Second TELSAM: R80S,UBA Domain: C610A,C644A	FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；100mM BisTris, pH 6.0, 960mM Mg-formate	Resolution 2.40 Å R-free 0.263
9NGE The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone Deposited 2025-02-22	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,L96E,V112E in ETV6, and L591V,C610A,C644A in TNK1 (Uniprot numbering)	PEG DI(HYDROXYETHYL)ETHER × 3 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene Glycol 3350	Resolution 2.02 Å R-free 0.230
9NGE The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone Deposited 2025-02-22	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R80S,L96E,V112E in ETV6, and L591V,C610A,C644A in TNK1 (Uniprot numbering)	K POTASSIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene Glycol 3350	Resolution 2.02 Å R-free 0.230
9O0H The ubiquitin-associated domain of human thirty-eight negative kinase 1, fused to the 3TEL crystallization chaperone via a 2-glycine linker Deposited 2025-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 590–666（77 aa） Fragment：TNK1 portion is the ubiquitin-associated domain	Mutation：V112E (Uniprot numbering) in the first ETV6 repeat, C610A,C644A (Uniprot numbering) in TNK1	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；1.5M Ammonium Chloride, 0.1M BIS-TRISpropane pH 7	Resolution 2.24 Å R-free 0.249
9Z2L The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to the 1TEL crystallization chaperone Deposited 2025-11-05	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R46S,V78E,L90V,C109A,C143A	SO4 SULFATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.6 M Magnesium Sulfate, 0.1 Sodium Acetate	Resolution 2.02 Å R-free 0.274
9Z2L The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to the 1TEL crystallization chaperone Deposited 2025-11-05	Different construct Different mutation/modification 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 590–666（77 aa）	Mutation：R46S,V78E,L90V,C109A,C143A	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.6 M Magnesium Sulfate, 0.1 Sodium Acetate	Resolution 2.02 Å R-free 0.274
9ZVU The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone, alternate crystal form Deposited 2025-12-30	Different construct Different mutation/modification 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 590–666（77 aa） Fragment：TNK1 UBA domain,TNK1 UBA domain	Mutation：R80S,L96E,V112E,L591V,C610A,C644A	TLA L(+)-TARTARIC ACID × 4 NA SODIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Sodium Tartrate, 16% PEG 3350 Monodisperse	Resolution 1.96 Å R-free 0.247
9ZVU The ubiquitin-associated domain of human thirty-eight negative kinase-1 rigidly fused to a double trigger variant of the 1TEL crystallization chaperone, alternate crystal form Deposited 2025-12-30	Different construct Different mutation/modification 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 590–666（77 aa） Fragment：TNK1 UBA domain,TNK1 UBA domain	Mutation：R80S,L96E,V112E,L591V,C610A,C644A	TLA L(+)-TARTARIC ACID × 3 NA SODIUM ION × 4 SO4 SULFATE ION × 2 TAR D(-)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M Sodium Tartrate, 16% PEG 3350 Monodisperse	Resolution 1.96 Å R-free 0.247

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

View Construct and Data Evidence

UniProt name	TNK1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–78； UniProt 589–666 Author chain B； PDBConstruct 1–78； UniProt 589–666

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7tcy
Deposition date deposition_date	2021-12-29
Structure title title	The ubiquitin-associated domain of human thirty-eight negative kinase I
Keywords keywords	Kinase, Ubiquitin-associated, UBA, ONCOPROTEIN, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.78 Å
Radius of gyration Rg (electron density) rg_electron	16.80 Å
Forward intensity I(0) i0	6233610.00
Molecular weight molecular_weight	17344.0 kDa
Excluded volume excluded_volume	21402 Å³
Envelope volume envelope_volume	25733 Å³
Hydration-shell volume shell_volume	13500 Å³
Envelope diameter envelope_diameter	66.0 Å
Shell Rg shell_rg	21.86 Å
Envelope Rg envelope_rg	17.08 Å
Shape Rg shape_rg	16.78 Å
Total Rg total_rg	17.72 Å
Total atoms total_atoms	2401
Residues n_residues	154
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

▼

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

Maximum dimension Dmax dmax	65.7 Å
Rg (real space) rg_real	17.76 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	6.2340e+06
I(0) uncertainty (real space) i0_real_error	1.0220e+05
Rg (reciprocal space) rg_reciprocal	17.76 Å
I(0) (reciprocal space) i0_reciprocal	6234000.0000
Solution quality estimate total_estimate	0.8274
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.8 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.193
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1875000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.619; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.909; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Non-receptor tyrosine-protein kinase TNK1
Molecular weight formula_weight	8753.9 kDa
EC 编号 ec_number	2.7.10.2
Mutation mutation	P589G, C610A, C644A
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	2617

GELQRKIMEVELSVHGVTHQEAQTALGATGGDVVSAIRNLKVDQLFHLSSRSRADAWRILEHYQWDLSAASRYVLARP

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

▶

8. Citations (1)

▶

Unit-cell length a length_a	53.734 Å
Unit-cell length b length_b	88.070 Å
Unit-cell length c length_c	26.497 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	1.540 Å
Low-resolution limit resolution_low	44.030 Å
R factor r_factor	0.1899
R_work r_work	0.1886
R_free r_free	0.2137

fit	/app/data/saxs_computation/tc/7tcy/7tcy.fit
pddf	/app/data/pr_computation/tc/7tcy/7tcy.pr.out
profile	/app/data/saxs_computation/tc/7tcy/7tcy.dat

The ubiquitin-associated domain of human thirty-eight negative kinase I

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

Non-receptor tyrosine-protein kinase TNK1

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