SAXSdb — 3bk3

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

Bone morphogenetic protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Crossveinless 2 × 2 （Q5D734） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Crossveinless 2 × 2 （Q5D734） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Crossveinless 2 × 1 （Q5D734） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Crossveinless 2 × 1 （Q5D734） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BMP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–114； UniProt 283–396 Author chain B； PDBConstruct 1–114； UniProt 283–396

Crossveinless 2

Danio rerio

UniProt Q5D734

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Bone morphogenetic protein 2 × 2 （P12643） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Bone morphogenetic protein 2 × 2 （P12643） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Bone morphogenetic protein 2 × 1 （P12643） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Bone morphogenetic protein 2 × 1 （P12643） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5D734_DANRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–67； UniProt 28–93 Author chain D； PDBConstruct 2–67； UniProt 28–93

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	3bk3
Deposition date deposition_date	2007-12-05
Structure title title	Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2
Keywords keywords	;TGF-beta superfamily, BMP modulator proteins, Chordin, BMP inhibitor, Chondrogenesis, Cleavage on pair of basic residues, Cytokine, Developmental protein, Differentiation, Glycoprotein, Growth factor, Osteogenesis, Polymorphism, Secreted, Hormone-growth Factor COMPLEX ;; Hormone/growth Factor
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.

3bk3__assembly_1__model_1

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

Download this curve (.dat)

3bk3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bk3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.39 Å
Rg (electron density)	29.48 Å
Total Rg	30.08 Å
Atom count	2588
Residues	342
Excluded volume	45889 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bk3__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bk3__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bk3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bk3__assembly_4__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	Bone morphogenetic protein 2
Molecular weight formula_weight	12875.9 kDa
Mutation mutation	F41M, Y91M
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	2635

QAKHKQRKRLKSSCKRHPLYVDFSDVGWNDWIVAPPGYHAMYCHGECPFPLADHLNSTNHAIVQTLVNSVNSKIPKACCVPTELSAISMLMLDENEKVVLKNYQDMVVEGCGCR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Crossveinless 2
Molecular weight formula_weight	7192.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

WLITGTEASCENEGEVLHIPNITDNPCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG

Source Source

Source organism organism	Danio rerio
Common name common_name	Zebrafish
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	47

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bk3a_
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.17.1.2 — Transforming growth factor (TGF)-beta

Domain ID domain_id	d3bk3b_
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.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (4 domains)

Domain ID domain_id	3bk3A00
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	3bk3B00
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	3bk3C00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	200 — Defensin A-like
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3bk3D00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	200 — Defensin A-like
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	83.750 Å
Unit-cell length b length_b	83.750 Å
Unit-cell length c length_c	139.850 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2050
R_work r_work	0.2030
R_free r_free	0.2450

Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2

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

Bone morphogenetic protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Crossveinless 2

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

3bk3__assembly_1__model_1

3bk3__assembly_1__model_1 | I(q)

3bk3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the complex of BMP-2 and the first Von Willebrand domain type C of Crossveinless-2

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

Bone morphogenetic protein 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

Crossveinless 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bk3__assembly_1__model_1

3bk3__assembly_1__model_1 | I(q)

3bk3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)