SAXSdb — 2ygq

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

WNT INHIBITORY FACTOR 1

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 3 其他Polymer 3	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 3 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 alpha-L-fucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	WIF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–315； UniProt 35–346

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	2ygq
Deposition date deposition_date	2011-04-19
Structure title title	WIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine
Keywords keywords	SIGNALING PROTEIN, WNT SIGNALING PATHWAY, WNT ANTAGONIST, MORPHOGEN, CANCER, GLYCOSAMINOGLYCAN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ygq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ygq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ygq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	29.24 Å
Rg (electron density)	27.60 Å
Total Rg	28.68 Å
Atom count	5907
Residues	723
Excluded volume	105080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ygq__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	WNT INHIBITORY FACTOR 1
Molecular weight formula_weight	35401.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1969

ETGSLYLWIDAHQARVLIGFEEDILIVSEGKMAPFTHDFRKAQQRMPAIPVNIHSMNFTWQAAGQAEYFYEFLSLRSLDKGIMADPTVNVPLLGTVPHKASVVQVGFPCLGKQDGVAAFEVDVIVMNSEGNTILKTPQNAIFFKTCQQAECPGGCRNGGFCNERRICECPDGFHGPHCEKALCTPRCMNGGLCVTPGFCICPPGFYGVNCDKANCSTTCFNGGTCFYPGKCICPPGLEGEQCEISKCPQPCRNGGKCIGKSKCKCSKGYQGDLCSKPVCEPGCGAHGTCHEPNKCQCQEGWHGRHCNKRYEASLIGTKHHHHHH

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	HOMO SAPIENS

Entity 2 Entity 2 branched

Description description	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
Molecular weight formula_weight	982.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ygqA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2170 — Wnt, WIF domain

Domain ID domain_id	2ygqA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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Unit-cell length a length_a	178.007 Å
Unit-cell length b length_b	178.007 Å
Unit-cell length c length_c	178.007 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	24

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	3.951 Å
Low-resolution limit resolution_low	39.804 Å
R factor r_factor	0.2985
R_work r_work	0.2970
R_free r_free	0.3306

WIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine

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

WNT INHIBITORY FACTOR 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ygq__assembly_1__model_1

2ygq__assembly_1__model_1 | I(q)

2ygq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

WIF domain-epidermal growth factor (EGF)-like domains 1-3 of human Wnt inhibitory factor 1 in complex with 1,2- dipalmitoylphosphatidylcholine

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

WNT INHIBITORY FACTOR 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ygq__assembly_1__model_1

2ygq__assembly_1__model_1 | I(q)

2ygq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)