SAXSdb — 4n4t

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

Tankyrase-1

Mus musculus

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 1097–1307	Fragment：UNP residues 1104-1314	ZN ZINC ION × 1 2GV (4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；0.2-0.4 M DiAmmonium Tartrate, 12.5-25% PEG 3350, pH 5.0-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.31 Å R-free 0.275
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1097–1307	Fragment：UNP residues 1104-1314	ZN ZINC ION × 1 2GV (4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；0.2-0.4 M DiAmmonium Tartrate, 12.5-25% PEG 3350, pH 5.0-6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.31 Å R-free 0.275

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 4N4T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3UTM Crystal structure of a mouse Tankyrase-Axin complex Deposited 2011-11-26	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 A 308–655（348 aa） Fragment：mTNKS1 ARC23 (UNP Residues 308-655) Chain B 308–655（348 aa） Fragment：mTNKS1 ARC23 (UNP Residues 308-655)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.6；295 K；0.06 M sodium citrate tribasic dihydrate pH 5.6, 1.2M ammonium acetate, 18% MPD, and 20mM DTT, EVAPORATION, temperature 295K	Resolution 2.00 Å R-free 0.238
5HKP Crystal structure of mouse Tankyrase/human TRF1 complex Deposited 2016-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 308–655（348 aa） Fragment：UNP residues 308-655 Chain B 308–655（348 aa） Fragment：UNP residues 308-655	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.035M Calcium Chloride dihydrate 0.07M MES monohydrate pH6.0 0.03M Tris pH8.5 31.5% v/v Polyethylene glycol 200 6% v/v Ethanol	Resolution 2.20 Å R-free 0.229
6CF6 RNF146 TBM-Tankyrase ARC2-3 complex Deposited 2018-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 308–655（348 aa） Chain B 308–655（348 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；30 mM sodium citrate pH 5.6, 60 mM ammonium acetate, 27% 2-methyl-2,4-pentanediol	Resolution 1.93 Å R-free 0.228

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

View Construct and Data Evidence

UniProt name	TNKS1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1097–1307 Author chain B； PDBConstruct 1–211； UniProt 1097–1307

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	4n4t
Deposition date deposition_date	2013-10-08
Structure title title	Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one]
Keywords keywords	tankyrase, PARP, Inhibitor, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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	26.34 Å
Radius of gyration Rg (electron density) rg_electron	25.77 Å
Forward intensity I(0) i0	41191600.00
Molecular weight molecular_weight	47720.0 kDa
Excluded volume excluded_volume	58882 Å³
Envelope volume envelope_volume	74251 Å³
Hydration-shell volume shell_volume	25167 Å³
Envelope diameter envelope_diameter	89.6 Å
Shell Rg shell_rg	31.72 Å
Envelope Rg envelope_rg	25.77 Å
Shape Rg shape_rg	25.68 Å
Total Rg total_rg	26.71 Å
Total atoms total_atoms	3360
Residues n_residues	411
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	84.3 Å
Rg (real space) rg_real	26.46 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	4.1190e+07
I(0) uncertainty (real space) i0_real_error	5.5870e+05
Rg (reciprocal space) rg_reciprocal	26.42 Å
I(0) (reciprocal space) i0_reciprocal	41190000.0000
Solution quality estimate total_estimate	0.6835
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.444
Kurtosis Kurtosis kurtosis	-0.426
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5612000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.928; Smooth: 0.850

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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	Tankyrase-1
Molecular weight formula_weight	25041.3 kDa
EC 编号 ec_number	2.4.2.30
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	3501

QGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTMKMAHAPPGHHSVIGRPSVNGLAYAEYVIYRGEQAYPEYLITYQIMKPEHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one
Molecular weight formula_weight	437.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4n4tA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4n4tB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	41.944 Å
Unit-cell length b length_b	77.879 Å
Unit-cell length c length_c	147.647 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.315 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2510
R_free r_free	0.2750

fit	/app/data/saxs_computation/n4/4n4t/4n4t.fit
pddf	/app/data/pr_computation/n4/4n4t/4n4t.pr.out
profile	/app/data/saxs_computation/n4/4n4t/4n4t.dat

Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one]

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

Tankyrase-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