SAXSdb — 6ndz

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

Frizzled-8

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 32–150	Mutation：N49Q	Designed repeat binding protein × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 ACT ACETATE ION × 3 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 32–150	Mutation：N49Q	Designed repeat binding protein × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 32–150	Mutation：N49Q	Designed repeat binding protein × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238

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 6NDZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21KR A Wnt3a/Fzd8-CRD/LRP6-E3E4 complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa） Chain I 31–155（125 aa）	Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.90 Å
21KS A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa） Chain I 31–155（125 aa）	Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.01 Å
21KT Wnt3a signalosome extracellular complex Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa）	Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.33 Å
5UN5 Frizzled-8 complex with designed surrogate Wnt agonist, crystal form 1 Deposited 2017-01-30	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 28–150（123 aa） Fragment：UNP residues 28-150 Chain B 28–150（123 aa） Fragment：UNP residues 28-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；42-49% PEG 400, 0.1 M Tris pH 7.8-8.2, 0.2 M NaCl	Resolution 2.99 Å R-free 0.250
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
8X0T Frizzled8 CRD in complex with pF8_AC3 Fab Deposited 2023-11-06	Different construct 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 30–153（124 aa）	Mutation：N49Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；32% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M MgCl2	Resolution 2.50 Å R-free 0.290

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

View Construct and Data Evidence

UniProt name	FZD8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 32–150 Author chain C； PDBConstruct 1–119； UniProt 32–150 Author chain E； PDBConstruct 1–119； UniProt 32–150

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	6ndz
Deposition date deposition_date	2018-12-14
Structure title title	Designed repeat protein in complex with Fz8
Keywords keywords	Frizzled, Designed protein, BIOSYNTHETIC PROTEIN, BIOSYNTHETIC PROTEIN-SIGNALING PROTEIN complex; BIOSYNTHETIC PROTEIN/SIGNALING PROTEIN
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	34.50 Å
Radius of gyration Rg (electron density) rg_electron	33.86 Å
Forward intensity I(0) i0	165119000.00
Molecular weight molecular_weight	101060.0 kDa
Excluded volume excluded_volume	126010 Å³
Envelope volume envelope_volume	165640 Å³
Hydration-shell volume shell_volume	41356 Å³
Envelope diameter envelope_diameter	114.4 Å
Shell Rg shell_rg	39.96 Å
Envelope Rg envelope_rg	33.26 Å
Shape Rg shape_rg	33.85 Å
Total Rg total_rg	34.37 Å
Total atoms total_atoms	7067
Residues n_residues	931
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	109.7 Å
Rg (real space) rg_real	34.44 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.6510e+08
I(0) uncertainty (real space) i0_real_error	2.7630e+06
Rg (reciprocal space) rg_reciprocal	34.48 Å
I(0) (reciprocal space) i0_reciprocal	165100000.0000
Solution quality estimate total_estimate	0.9085
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.5 Å
Skewness Skewness skewness	0.186
Kurtosis Kurtosis kurtosis	-0.641
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13490000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.941

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Frizzled-8
Molecular weight formula_weight	14602.7 kDa
Mutation mutation	N49Q
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	7282

ELACQEITVPLCKGIGYQYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLKFFLCSMYTPICLEDYKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQGNPDTLCMDHHHHHH

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Designed repeat binding protein
Molecular weight formula_weight	20862.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

MGSELGKRLIMAALDGNKDRVKDLIENGADVNASLVSGATPLHAAAMNGHKEVVKLLISKGADVNAQSAAGSTPLAAAAINGHKEVVKLLISKGADVNAVTAAGMTPLHAAAANGHKEVVKLLISKGADVNAKADRGMTPLHFAAWRGHKEVVKLLISKGADLNTSAKDGATPLDMARESGNEEVVKLLEKQLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 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	215

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6ndzB00
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	6ndzD00
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	6ndzF00
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	79.930 Å
Unit-cell length b length_b	109.015 Å
Unit-cell length c length_c	114.373 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.264 Å
Low-resolution limit resolution_low	42.778 Å
R factor r_factor	0.2130
R_work r_work	0.2118
R_free r_free	0.2377

fit	/app/data/saxs_computation/nd/6ndz/6ndz.fit
pddf	/app/data/pr_computation/nd/6ndz/6ndz.pr.out
profile	/app/data/saxs_computation/nd/6ndz/6ndz.dat

Designed repeat protein in complex with Fz8

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

Frizzled-8

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)