SAXSdb — 5vt2

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

Growth/differentiation factor 15

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GDF15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 197–308 Author chain B； PDBConstruct 1–112； UniProt 197–308

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	5vt2
Deposition date deposition_date	2017-05-15
Structure title title	Crystal structure of growth differentiation factor
Keywords keywords	TGF-beta family, SIGNALING PROTEIN; 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.

5vt2__assembly_1__model_1

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

Download this curve (.dat)

5vt2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vt2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.35 Å
Rg (electron density)	20.08 Å
Total Rg	20.70 Å
Atom count	1674
Residues	216
Excluded volume	29810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vt2__assembly_1__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	Growth/differentiation factor 15
Molecular weight formula_weight	12303.2 kDa
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	1773

ARNGDHCPLGPGRCCRLHTVRASLEDLGWADWVLSPREVQVTMCIGACPSQFRAANMHAQIKTSLHRLKPDTVPAPCCVPASYNPMVLIQKTDTGVSLQTYDDLLAKDCHCI

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5vt2a_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d5vt2b_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

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Unit-cell length a length_a	64.720 Å
Unit-cell length b length_b	64.720 Å
Unit-cell length c length_c	172.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2083
R_work r_work	0.2065
R_free r_free	0.2418

Crystal structure of growth differentiation factor

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

Growth/differentiation factor 15

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

5vt2__assembly_1__model_1

5vt2__assembly_1__model_1 | I(q)

5vt2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Crystal structure of growth differentiation factor

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

Growth/differentiation factor 15

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

5vt2__assembly_1__model_1

5vt2__assembly_1__model_1 | I(q)

5vt2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)