SAXSdb — 5wbs

▼

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

Frizzled-7,inhibitor peptide Fz7-21

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 30–178 Chain B； UniProt 30–178	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；1-propanol 14% (v/v; cat. no. 09158; Fluka), 9% PEG5000 MME (cat. no. HR-2-615; Hampton Research), and 0.1 M MES at pH 6.9 (cat. no. HR2-243; Hampton Research)	Resolution 2.88 Å R-free 0.244
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 30–178 Chain D； UniProt 30–178	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；1-propanol 14% (v/v; cat. no. 09158; Fluka), 9% PEG5000 MME (cat. no. HR-2-615; Hampton Research), and 0.1 M MES at pH 6.9 (cat. no. HR2-243; Hampton Research)	Resolution 2.88 Å R-free 0.244
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 30–178 Chain F； UniProt 30–178	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；1-propanol 14% (v/v; cat. no. 09158; Fluka), 9% PEG5000 MME (cat. no. HR-2-615; Hampton Research), and 0.1 M MES at pH 6.9 (cat. no. HR2-243; Hampton Research)	Resolution 2.88 Å R-free 0.244
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 30–178 Chain H； UniProt 30–178	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；1-propanol 14% (v/v; cat. no. 09158; Fluka), 9% PEG5000 MME (cat. no. HR-2-615; Hampton Research), and 0.1 M MES at pH 6.9 (cat. no. HR2-243; Hampton Research)	Resolution 2.88 Å R-free 0.244

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 5WBS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5T44 Crystal structure of Frizzled 7 CRD Deposited 2016-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–168（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；0.1M MES at pH6.9, 12% 1-propanol, 10% PEG 500MME	Resolution 1.99 Å R-free 0.252
5T44 Crystal structure of Frizzled 7 CRD Deposited 2016-08-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 31–168（138 aa） Chain B 31–168（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；0.1M MES at pH6.9, 12% 1-propanol, 10% PEG 500MME	Resolution 1.99 Å R-free 0.252
5T44 Crystal structure of Frizzled 7 CRD Deposited 2016-08-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–168（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；277 K；0.1M MES at pH6.9, 12% 1-propanol, 10% PEG 500MME	Resolution 1.99 Å R-free 0.252
5URV Crystal structure of Frizzled 7 CRD in complex with C24 fatty acid Deposited 2017-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–168（139 aa） Chain B 30–168（139 aa）	Not recorded	NER (15E)-TETRACOS-15-ENOIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 8 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.1M MES sodium salt pH 6.5, 2.0M Ammonium sulfate, 5%(w/v) PEG 400	Resolution 2.20 Å R-free 0.210
6NE2 Designed repeat protein in complex with Fz7 Deposited 2018-12-15	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 A 46–163（118 aa）	Not recorded	ACT ACETATE ION × 9 SO4 SULFATE ION × 10 EDO 1,2-ETHANEDIOL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Sodium Acetate: HCl, pH 4.5, 2 M Ammonium Sulfate	Resolution 1.30 Å R-free 0.184
6NE4 Designed repeat protein specifically in complex with Fz7CRD Deposited 2018-12-16	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 A 46–163（118 aa）	Not recorded	SO4 SULFATE ION × 14 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M Na2HPO4, citric acid, pH 4.2 and 2M Ammonium sulfate	Resolution 1.65 Å R-free 0.186
6O3A Crystal structure of Frizzled 7 CRD in complex with F7.B Fab Deposited 2019-02-26	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 E 42–179（138 aa）	Not recorded	CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 6 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 10；293 K；0.1 M CAPS, pH 10.5, 20% (w/v) PEG 3350, 0.2 M NaCl	Resolution 2.10 Å R-free 0.242
6O3B Crystal structure of Frizzled 7 CRD in complex with F6 Fab Deposited 2019-02-26	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 C 42–179（138 aa）	Not recorded	GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.2 M Na2HPO4, 20% (w/v) PEG 3350	Resolution 2.50 Å R-free 0.283
6O3B Crystal structure of Frizzled 7 CRD in complex with F6 Fab Deposited 2019-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 42–179（138 aa）	Not recorded	GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.2 M Na2HPO4, 20% (w/v) PEG 3350	Resolution 2.50 Å R-free 0.283
8QEO cryo-EM structure complex of Frizzled-7 and Clostridioides difficile toxin B Deposited 2023-09-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–574（542 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；100 mM TRIS-HCl pH 7.5 200 mM NaCl 0.002% LMNG 0.0002% CHS 0.0002% GDN cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
8YY8 Fzd7 -Gs complex Deposited 2024-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 38–574（537 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
9EPO High resolution structure of FZD7 in inactive conformation Deposited 2024-03-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–574（542 aa） Chain D 33–574（542 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 4 PLM PALMITIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.90 Å
9EW2 High resolution structure of FZD7 in complex with miniGs protein Deposited 2024-04-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 38–574（537 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9RHG FZD7 in complex with negative allosteric modulator C407 Deposited 2025-06-09	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–574（542 aa） Chain B 33–574（542 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 4 A1JGQ ethyl 3-[2-[(2-fluorophenyl)amino]-2-oxidanylidene-ethyl]-5-methyl-4-oxidanylidene-thieno[2,3-d]pyrimidine-6-carboxylate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FZD7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 30–178 Author chain B； PDBConstruct 1–149； UniProt 30–178 Author chain C； PDBConstruct 1–149； UniProt 30–178 Author chain D； PDBConstruct 1–149； UniProt 30–178 Author chain E； PDBConstruct 1–149； UniProt 30–178 Author chain F； PDBConstruct 1–149； UniProt 30–178 Author chain G； PDBConstruct 1–149； UniProt 30–178 Author chain H； PDBConstruct 1–149； UniProt 30–178

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	5wbs
Deposition date deposition_date	2017-06-29
Structure title title	Crystal structure of Frizzled-7 CRD with an inhibitor peptide Fz7-21
Keywords keywords	Frizzled, Wnt signaling, inhibitor, dimerization, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	43.64 Å
Radius of gyration Rg (electron density) rg_electron	43.68 Å
Forward intensity I(0) i0	226802000.00
Molecular weight molecular_weight	119570.0 kDa
Excluded volume excluded_volume	148160 Å³
Envelope volume envelope_volume	220260 Å³
Hydration-shell volume shell_volume	45736 Å³
Envelope diameter envelope_diameter	152.4 Å
Shell Rg shell_rg	43.68 Å
Envelope Rg envelope_rg	43.01 Å
Shape Rg shape_rg	43.68 Å
Total Rg total_rg	43.68 Å
Total atoms total_atoms	8359
Residues n_residues	1057
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	153.4 Å
Rg (real space) rg_real	43.76 Å
Rg uncertainty (real space) rg_real_error	1.79 Å
I(0) (real space) i0_real	2.2680e+08
I(0) uncertainty (real space) i0_real_error	4.9780e+06
Rg (reciprocal space) rg_reciprocal	43.64 Å
I(0) (reciprocal space) i0_reciprocal	226800000.0000
Solution quality estimate total_estimate	0.7946
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	55.4 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10900000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	62.610 Å
Unit-cell length b length_b	164.650 Å
Unit-cell length c length_c	97.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.880 Å
Low-resolution limit resolution_low	38.717 Å
R factor r_factor	0.2013
R_work r_work	0.1991
R_free r_free	0.2443

Description description	Frizzled-7,inhibitor peptide Fz7-21
Molecular weight formula_weight	20105.3 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	8360

Crystal structure of Frizzled-7 CRD with an inhibitor peptide Fz7-21

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

Frizzled-7,inhibitor peptide Fz7-21

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	Spodoptera frugiperda

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

fit	/app/data/saxs_computation/wb/5wbs/5wbs.fit
pddf	/app/data/pr_computation/wb/5wbs/5wbs.pr.out
profile	/app/data/saxs_computation/wb/5wbs/5wbs.dat