SAXSdb — 7poj

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

Bone morphogenetic protein 10

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	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 317–424 Chain B； UniProt 317–424 Chain C； UniProt 22–316 Chain D； UniProt 22–316	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；20% PEG3350 0.2 M ammonium tartrate dibasic	Resolution 3.50 Å R-free 0.300

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 7POJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6SF1 Bone morphogenetic protein 10 (BMP10) complexed with extracellular domain of activin receptor-like kinase 1 (ALK1). Deposited 2019-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 317–424（108 aa）	Not recorded	NI NICKEL (II) ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17% PEG 3350, 0.175 M NH4I, 0.1 M HEPES pH 7.8	Resolution 2.80 Å R-free 0.279
6SF3 Bone morphogenetic protein 10 (BMP10) in complex with extracellular domain of activin receptor-like kinase 1 (ALK1) at 2.3 Angstrom Deposited 2019-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.07 M Amino acids (0.014 M DL-Glutamic acids monohydrate; 0.014 M DL-Alanine; 0.014 M Glycine; 0.014 M DL-Lysine monohydrochloride; 0.014 M DL-Serine), 0.07 M Buffer System 3 (0.07 M Tris(base)/BICINE), 35% Precipitant Mix 4 (9% v/v MPD, 9% w/v PEG 1000, 9% w/ PEG3350)	Resolution 2.30 Å R-free 0.243
7POI Prodomain bound BMP10 crystal form 1 Deposited 2021-09-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa） Chain C 22–316（295 aa） Chain D 22–316（295 aa）	Not recorded	TAR D(-)-TARTARIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；294.15 K；19% PEG 3350 0.15 M Ammonium tartrate dibasic 0.02 M Sodium cacodylate trihydrate	Resolution 2.90 Å R-free 0.268
7PPA High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294.15 K；14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate	Resolution 1.48 Å R-free 0.207
7PPB 2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294.15 K；14% PEG 3350 0.14 M KCl	Resolution 2.40 Å R-free 0.235
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	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 A 317–424（108 aa） Chain B 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 317–424（108 aa） Chain D 317–424（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate	Resolution 3.60 Å R-free 0.282
9DPY BMP-10 with BMP-9 Crystal Contacts Deposited 2024-09-23	Different construct Different mutation/modification 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 320–424（105 aa） Chain B 320–424（105 aa）	Mutation：N357F, Y358F, A374T, Y409L, F411Y Mutation：N357F, Y358F, A374T, Y409L, F411Y	PO4 PHOSPHATE ION × 13 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；25% (v/v) 1,2-propanediol, 100 mM sodium phosphate dibasic/potassium phosphate monobasic pH 6.2, 10% (v/v) glycerol	Resolution 1.77 Å R-free 0.251

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMP10_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 317–424 Author chain B； PDBConstruct 1–108； UniProt 317–424 Author chain C； PDBConstruct 1–295； UniProt 22–316 Author chain D； PDBConstruct 1–295； UniProt 22–316

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	7poj
Deposition date deposition_date	2021-09-09
Structure title title	Prodomain bound BMP10 crystal form 2
Keywords keywords	BMP10 bone morphogenetic protein prodomain TGFbeta signalling, CYTOKINE; CYTOKINE
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	34.08 Å
Radius of gyration Rg (electron density) rg_electron	34.23 Å
Forward intensity I(0) i0	47299100.00
Molecular weight molecular_weight	56001.0 kDa
Excluded volume excluded_volume	70603 Å³
Envelope volume envelope_volume	99069 Å³
Hydration-shell volume shell_volume	25264 Å³
Envelope diameter envelope_diameter	122.6 Å
Shell Rg shell_rg	38.68 Å
Envelope Rg envelope_rg	33.91 Å
Shape Rg shape_rg	34.27 Å
Total Rg total_rg	34.43 Å
Total atoms total_atoms	3941
Residues n_residues	481
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	113.2 Å
Rg (real space) rg_real	34.34 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	4.7300e+07
I(0) uncertainty (real space) i0_real_error	8.1170e+05
Rg (reciprocal space) rg_reciprocal	34.18 Å
I(0) (reciprocal space) i0_reciprocal	47290000.0000
Solution quality estimate total_estimate	0.8159
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.584
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6124000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.573

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Bone morphogenetic protein 10
Molecular weight formula_weight	12177.2 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	3942

NAKGNYCKRTPLYIDFKEIGWDSWIIAPPGYEAYECRGVCNYPLAEHLTPTKHAIIQALVHLKNSQKASKACCVPTKLEPISILYLDKGVVTYKFKYEGMAVSECGCR

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Bone morphogenetic protein 10
Molecular weight formula_weight	33813.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SPIMNLEQSPLEEDMSLFGDVFSEQDGVDFNTLLQSMKDEFLKTLNLSDIPTQDSAKVDPPEYMLELYNKFATDRTSMPSANIIRSFKNEDLFSQPVSFNGLRKYPLLFNVSIPHHEEVIMAELRLYTLVQRDRMIYDGVDRKITIFEVLESKGDNEGERNMLVLVSGEIYGTNSEWETFDVTDAIRRWQKSGSSTHQLEVHIESKHDEAEDASSGRLEIDTSAQNKHNPLLIVFSDDQSSDKERKEELNEMISHEQLPELDNLGLDSFSSGPGEEALLQMRSNIIYDSTARIRR

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	Homo sapiens

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 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	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	143.351 Å
Unit-cell length b length_b	144.108 Å
Unit-cell length c length_c	82.129 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	101.630 Å
R factor r_factor	0.2758
R_work r_work	0.2746
R_free r_free	0.2998

fit	/app/data/saxs_computation/po/7poj/7poj.fit
pddf	/app/data/pr_computation/po/7poj/7poj.pr.out
profile	/app/data/saxs_computation/po/7poj/7poj.dat

Prodomain bound BMP10 crystal form 2

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

Bone morphogenetic protein 10

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)