SAXSdb — 5hk5

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

Gremlin-2

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Growth/differentiation factor 5 × 2 （P43026）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Growth/differentiation factor 5 × 2 （P43026）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Growth/differentiation factor 5 × 2 （P43026）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Growth/differentiation factor 5 × 2 （P43026）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GREM2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–147； UniProt 22–168 Author chain F； PDBConstruct 1–147； UniProt 22–168 Author chain G； PDBConstruct 1–147； UniProt 22–168 Author chain H； PDBConstruct 1–147； UniProt 22–168

Growth/differentiation factor 5

Homo sapiens

UniProt P43026

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Gremlin-2 × 2 （O88273）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Gremlin-2 × 2 （O88273）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Gremlin-2 × 2 （O88273）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Gremlin-2 × 2 （O88273）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GDF5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 382–501 Author chain B； PDBConstruct 1–120； UniProt 382–501 Author chain C； PDBConstruct 1–120； UniProt 382–501 Author chain D； PDBConstruct 1–120； UniProt 382–501

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	5hk5
Deposition date deposition_date	2016-01-13
Structure title title	Structure of the Grem2-GDF5 Inhibitory Complex
Keywords keywords	DAN-family, Bone Morphogenetic Proteins, CYTOKINE; CYTOKINE
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.

5hk5__assembly_1__model_1

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

Download this curve (.dat)

5hk5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hk5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.04 Å
Rg (electron density)	33.47 Å
Total Rg	33.67 Å
Atom count	3743
Residues	467
Excluded volume	66630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hk5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5hk5__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5hk5__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5hk5__assembly_4__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	Gremlin-2
Molecular weight formula_weight	17007.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H
Atom count atom_count	7436

RKNRPAGAIPSPYKDGSSNNSERWHHQIKEVLASSQEALVVTERKYLKSDWCKTQPLRQTVSEEGCRSRTILNRFCYGQCNSFYIPRHVKKEEDSFQSCAFCKPQRVTSVIVELECPGLDPPFRIKKIQKVKHCRCMSVNLSDSDKQ

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Growth/differentiation factor 5
Molecular weight formula_weight	13598.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

APLATRQGKRPSKNLKARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR

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

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5hk5a_
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	d5hk5b_
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	d5hk5c_
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	d5hk5d_
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

CATH v4.4 (7 domains)

Domain ID domain_id	5hk5A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5C00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5D00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5E00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5F00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	5hk5G00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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Unit-cell length a length_a	114.721 Å
Unit-cell length b length_b	125.791 Å
Unit-cell length c length_c	125.930 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	16

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	50.550 Å
R factor r_factor	0.2625
R_work r_work	0.2614
R_free r_free	0.2824

Structure of the Grem2-GDF5 Inhibitory Complex

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

Gremlin-2

State in the Current Structure

Other States of the Same Protein in the Database

Growth/differentiation factor 5

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

5hk5__assembly_1__model_1

5hk5__assembly_1__model_1 | I(q)

5hk5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Structure of the Grem2-GDF5 Inhibitory Complex

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

Gremlin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Growth/differentiation factor 5

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

5hk5__assembly_1__model_1

5hk5__assembly_1__model_1 | I(q)

5hk5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)