SAXSdb — 6cf6

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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 308–655 Chain B； UniProt 308–655	Not recorded	RNF146 × 2	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

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 6CF6	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 oligomeric state 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
4N4T 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] Deposited 2013-10-08	Different construct Different mutation/modification 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 1097–1307（211 aa） Fragment：UNP residues 1104-1314	Not recorded	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
4N4T 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] Deposited 2013-10-08	Different construct Different mutation/modification 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 1097–1307（211 aa） Fragment：UNP residues 1104-1314	Not recorded	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
5HKP Crystal structure of mouse Tankyrase/human TRF1 complex Deposited 2016-01-14	Different construct 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

3 other PDB entries and 4 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 1–348； UniProt 308–655 Author chain B； PDBConstruct 1–348； UniProt 308–655

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	6cf6
Deposition date deposition_date	2018-02-13
Structure title title	RNF146 TBM-Tankyrase ARC2-3 complex
Keywords keywords	complex, E3 ligase, PARP, ankyrin repeat, 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	34.03 Å
Radius of gyration Rg (electron density) rg_electron	33.95 Å
Forward intensity I(0) i0	85991000.00
Molecular weight molecular_weight	71700.0 kDa
Excluded volume excluded_volume	89065 Å³
Envelope volume envelope_volume	113530 Å³
Hydration-shell volume shell_volume	30254 Å³
Envelope diameter envelope_diameter	128.0 Å
Shell Rg shell_rg	36.67 Å
Envelope Rg envelope_rg	34.57 Å
Shape Rg shape_rg	33.94 Å
Total Rg total_rg	34.20 Å
Total atoms total_atoms	5030
Residues n_residues	661
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	119.6 Å
Rg (real space) rg_real	34.14 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	8.5990e+07
I(0) uncertainty (real space) i0_real_error	1.4640e+06
Rg (reciprocal space) rg_reciprocal	34.07 Å
I(0) (reciprocal space) i0_reciprocal	85990000.0000
Solution quality estimate total_estimate	0.8474
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.3 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6095000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.782; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.777; Smooth: 0.890

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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	Tankyrase-1
Molecular weight formula_weight	37902.4 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	5338

GKSALDLADPSAKAVLTGEYKKDELLEAARSGNEEKLMALLTPLNVNCHASDGRKSTPLHLAAGYNRVRIVQLLLQHGADVHAKDKGGLVPLHNACSYGHYEVTELLLKHGACVNAMDLWQFTPLHEAASKNRVEVCSLLLSHGADPTLVNCHGKSAVDMAPTPELRERLTYEFKGHSLLQAAREADLAKVKKTLALEIINFKQPQSHETALHCAVASLHPKRKQVAELLLRKGANVNEKNKDFMTPLHVAAERAHNDVMEVLHKHGAKMNALDSLGQTALHRAALAGHLQTCRLLLSYGSDPSIISLQGFTAAQMGNEAVQQILSESTPMRTSDVDYRLLEASKAGD

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 BL21

Entity 2 Entity 2 polymer

Description description	RNF146
Molecular weight formula_weight	1293.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

NLARESSADGADS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6cf6A01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	6cf6A02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	6cf6B01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

Domain ID domain_id	6cf6B02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (1)

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Unit-cell length a length_a	134.019 Å
Unit-cell length b length_b	103.284 Å
Unit-cell length c length_c	75.163 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.93 °
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	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1970
R_work r_work	0.1954
R_free r_free	0.2279

fit	/app/data/saxs_computation/cf/6cf6/6cf6.fit
pddf	/app/data/pr_computation/cf/6cf6/6cf6.pr.out
profile	/app/data/saxs_computation/cf/6cf6/6cf6.dat

RNF146 TBM-Tankyrase ARC2-3 complex

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)