SAXSdb — 1lx5

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

bone morphogenetic protein 7

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	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 293–431	Not recorded	Activin Type II Receptor × 2 （P27038） ;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；1M sodium acetate, 0.1M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.30 Å R-free 0.279

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 1LX5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BMP BONE MORPHOGENETIC PROTEIN-7 Deposited 1995-12-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 293–431（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.308
1LXI Refinement of BMP7 crystal structure Deposited 2002-06-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 293–431（139 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；20% MPD, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.244
1M4U Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin Deposited 2002-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 293–431（139 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.6 M disodium, 1.0 M monopotassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.42 Å R-free 0.273

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMP7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–139； UniProt 293–431

Activin Type II Receptor

Mus musculus

UniProt P27038

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 20–121	Fragment：Extracellular Ligand Binding Domain, C-terminal truncation	bone morphogenetic protein 7 × 2 （P18075） ;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；1M sodium acetate, 0.1M imidazole, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.30 Å R-free 0.279

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 1LX5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BTE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTIVIN RECEPTOR Deposited 1998-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–121（97 aa） Fragment：LIGAND-BINDING DOMAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；100 MM SODIUM ACETATE, PH 4.5, 5% PEG 8000, 0.5M NACL	Resolution 1.50 Å R-free 0.222
1BTE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE TYPE II ACTIVIN RECEPTOR Deposited 1998-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 25–121（97 aa） Fragment：LIGAND-BINDING DOMAIN	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；100 MM SODIUM ACETATE, PH 4.5, 5% PEG 8000, 0.5M NACL	Resolution 1.50 Å R-free 0.222
2GOO Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD Deposited 2006-04-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 20–121（102 aa） Fragment：Residues 20-121 Chain F 20–121（102 aa） Fragment：Residues 20-121	Not recorded	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；4M sodium formate, 100mM Hepes, 3% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.259

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AVR2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 20–121

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	1lx5
Deposition date deposition_date	2002-06-04
Structure title title	Crystal Structure of the BMP7/ActRII Extracellular Domain Complex
Keywords keywords	LIGAND-RECEPTOR COMPLEX, GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX; GROWTH FACTOR/GROWTH FACTOR RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	21.43 Å
Radius of gyration Rg (electron density) rg_electron	21.28 Å
Forward intensity I(0) i0	11412400.00
Molecular weight molecular_weight	24266.0 kDa
Excluded volume excluded_volume	29894 Å³
Envelope volume envelope_volume	37331 Å³
Hydration-shell volume shell_volume	16264 Å³
Envelope diameter envelope_diameter	78.1 Å
Shell Rg shell_rg	25.55 Å
Envelope Rg envelope_rg	21.53 Å
Shape Rg shape_rg	21.30 Å
Total Rg total_rg	21.82 Å
Total atoms total_atoms	1695
Residues n_residues	198
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

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.5 Å
Rg (real space) rg_real	21.63 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.1410e+07
I(0) uncertainty (real space) i0_real_error	1.5670e+05
Rg (reciprocal space) rg_reciprocal	21.60 Å
I(0) (reciprocal space) i0_reciprocal	11410000.0000
Solution quality estimate total_estimate	0.8166
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.556
Kurtosis Kurtosis kurtosis	-0.176
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1070000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.690; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	bone morphogenetic protein 7
Molecular weight formula_weight	15699.7 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	1695

STGSKQRSQNRSKTPKNQEALRMANVAENSSSDQRQACKKHELYVSFRDLGWQDWIIAPEGYAAYYCEGECAFPLNSYMNATNHAIVQTLVHFINPETVPKPCCAPTQLNAISVLYFDDSSNVILKKYRNMVVRACGCH

来源 Source

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	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Activin Type II Receptor
Molecular weight formula_weight	12019.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AILGRSETQECLFFNANWERDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCIEKKDSPEVYFCCCEGNMCNEKFSYFPEME

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Pichia pastoris

Entity 3 Entity 3 branched

Description description	;alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
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

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lx5a_
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	d1lx5b_
Class class	g — Small proteins
Fold Fold fold	g.7 — Snake toxin-like
Superfamily Superfamily superfamily	g.7.1 — Snake toxin-like
Family Family family	g.7.1.3 — Extracellular domain of cell surface receptors

CATH v4.4 (2 domains)

Domain ID domain_id	1lx5A00
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	1lx5B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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8. Citations (1)

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Unit-cell length a length_a	140.920 Å
Unit-cell length b length_b	140.920 Å
Unit-cell length c length_c	90.810 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 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	27.120 Å
R factor r_factor	0.2400
R_work r_work	0.2380
R_free r_free	0.2790

fit	/app/data/saxs_computation/lx/1lx5/1lx5.fit
pddf	/app/data/pr_computation/lx/1lx5/1lx5.pr.out
profile	/app/data/saxs_computation/lx/1lx5/1lx5.dat

Crystal Structure of the BMP7/ActRII Extracellular Domain Complex

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

bone morphogenetic protein 7

State in the Current Structure

Other States of the Same Protein in the Database

Activin Type II Receptor

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)