SAXSdb — 9ydy

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

Transforming acidic coiled-coil-containing protein 3

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 758–838 Chain B； UniProt 758–838	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1 M imidazole, 50% (+/-)-2-Methyl-2,4-pentanediol (MPD)	Resolution 2.30 Å R-free 0.264

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 9YDY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LXN Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 758–838（81 aa） Chain B 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.08 Å R-free 0.285
5LXN Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 758–838（81 aa） Chain D 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.08 Å R-free 0.285
5LXN Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 758–838（81 aa） Chain F 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.08 Å R-free 0.285
5LXN Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 758–838（81 aa） Chain H 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.08 Å R-free 0.285
5LXO Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 758–838（81 aa） Chain B 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.18 Å R-free 0.285
5LXO Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 758–838（81 aa） Chain D 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.18 Å R-free 0.285
5LXO Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 758–838（81 aa） Chain F 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.18 Å R-free 0.285
5LXO Coiled-coil protein Deposited 2016-09-22	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 758–838（81 aa） Chain H 758–838（81 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289.15 K；35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5	Resolution 2.18 Å R-free 0.285
5ODT Aurora-A in complex with TACC3 Deposited 2017-07-06	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 519–563（45 aa） Fragment：UNP residues 519-563	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；0.1 M Bis-Tris pH 5.5, 2 M Ammonium sulphate	Resolution 2.02 Å R-free 0.211

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

View Construct and Data Evidence

UniProt name	TACC3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–81； UniProt 758–838 Author chain B； PDBConstruct 1–81； UniProt 758–838

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	9ydy
Deposition date deposition_date	2025-09-23
Structure title title	C-terminal coiled coil dimer of human TACC3
Keywords keywords	coiled-coiled, coactivator, PROTEIN BINDING; PROTEIN BINDING
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	21.52 Å
Radius of gyration Rg (electron density) rg_electron	22.05 Å
Forward intensity I(0) i0	2858550.00
Molecular weight molecular_weight	11532.0 kDa
Excluded volume excluded_volume	14327 Å³
Envelope volume envelope_volume	18785 Å³
Hydration-shell volume shell_volume	9135 Å³
Envelope diameter envelope_diameter	84.0 Å
Shell Rg shell_rg	24.23 Å
Envelope Rg envelope_rg	22.97 Å
Shape Rg shape_rg	21.98 Å
Total Rg total_rg	22.63 Å
Total atoms total_atoms	1644
Residues n_residues	100
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	84.2 Å
Rg (real space) rg_real	22.18 Å
Rg uncertainty (real space) rg_real_error	1.21 Å
I(0) (real space) i0_real	2.8590e+06
I(0) uncertainty (real space) i0_real_error	4.4130e+04
Rg (reciprocal space) rg_reciprocal	22.06 Å
I(0) (reciprocal space) i0_reciprocal	2858000.0000
Solution quality estimate total_estimate	0.6763
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.9 Å
Skewness Skewness skewness	0.758
Kurtosis Kurtosis kurtosis	-0.047
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	237100.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.262; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.017; Smooth: 0.984

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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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8. Citations (1)

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Unit-cell length a length_a	263.079 Å
Unit-cell length b length_b	23.827 Å
Unit-cell length c length_c	31.856 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	32.870 Å
R factor r_factor	0.2511
R_work r_work	0.2497
R_free r_free	0.2637

Description description	Transforming acidic coiled-coil-containing protein 3
Molecular weight formula_weight	9354.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1667

C-terminal coiled coil dimer of human TACC3

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

Transforming acidic coiled-coil-containing protein 3

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

fit	/app/data/saxs_computation/yd/9ydy/9ydy.fit
pddf	/app/data/pr_computation/yd/9ydy/9ydy.pr.out
profile	/app/data/saxs_computation/yd/9ydy/9ydy.dat