SAXSdb — 5ngv

▼

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

Activin receptor type-2B

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 24–117	Fragment：LIGAND BINDING domain	anti-human ActRIIB mAb BYM338 heavy-chain × 1 anti-human ActRIIB mAb BYM338 light-chain × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.4；293 K；0.1M PHOSPHATE-CITRATE, 40% PEG 300	Resolution 2.00 Å R-free 0.198

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 5NGV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QLU Crystal structure of Activin receptor type II kinase domain from human Deposited 2007-07-13	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 190–487（298 aa） Fragment：Protein kinase domain	Not recorded	SO4 SULFATE ION × 2 ADE ADENINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；45mM MES, 90mM ammonium sulfate, 11% polyethylene glycol monomethyl ether 5000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.283
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	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 E 19–134（116 aa） Fragment：Extracellular domain Chain F 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	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 K 19–134（116 aa） Fragment：Extracellular domain Chain L 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain Q 19–134（116 aa） Fragment：Extracellular domain Chain R 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain W 19–134（116 aa） Fragment：Extracellular domain Chain X 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain e 19–134（116 aa） Fragment：Extracellular domain Chain f 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
4FAO Specificity and Structure of a high affinity Activin-like 1 (ALK1) signaling complex Deposited 2012-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain k 19–134（116 aa） Fragment：Extracellular domain Chain l 19–134（116 aa） Fragment：Extracellular domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；20% PEG 3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 6.5, vapor diffusion, temperature 293K	Resolution 3.36 Å R-free 0.261
5NHR CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM Deposited 2017-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 24–117（94 aa） Fragment：VL, UNP residues 24-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE	Resolution 3.35 Å R-free 0.229
5NHR CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, CUBIC CRYSTAL FORM Deposited 2017-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–117（94 aa） Fragment：VL, UNP residues 24-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.4M AMMONIUM SULFATE, 0.1M SODIUM CITRATE	Resolution 3.35 Å R-free 0.229
7MRZ Structure of GDF11 bound to fused ActRIIB-ECD and Alk4-ECD with Anti-ActRIIB Fab fragment Deposited 2021-05-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain C 19–134（116 aa） Fragment：Extracellular domains of both proteins in the fused construct	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 0.9M ammonium sulfate, 0.9 M KCl	Resolution 3.00 Å R-free 0.327
7OLY Structure of activin A in complex with an ActRIIB-Alk4 fusion reveal insight into activin receptor interactions Deposited 2021-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain C 19–134（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；17.7 mg/ml complex in 20 mM HEPES, 200 mM NaCl pH 7.5. 100 + 100 nl sitting drop in a MRC 3-well plate with reservoir 0.1 M Na cacodylate pH 6.5 and 17 % (w/v) PEG 4000).	Resolution 3.27 Å R-free 0.269
9D20 Crystal structure of DLK1 in complex with ACVR2B Deposited 2024-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 25–118（94 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 3 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242
9D20 Crystal structure of DLK1 in complex with ACVR2B Deposited 2024-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–118（94 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 2 FUC alpha-L-fucopyranose × 1 BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；293 K；2.1 M (NH4)2SO4, 0.1 M HEPES PH 7.6 and 2.5% polyethylene glycol (PEG) 400	Resolution 2.67 Å R-free 0.242
9N4K CryoEM structure of ALK2-ActRIIB bound to BMP6 Deposited 2025-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 19–134（116 aa） Chain F 19–134（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BMA beta-D-mannopyranose × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；50mM Tris-HCL, 100mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

7 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AVR2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–99； UniProt 24–117

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ngv
Deposition date deposition_date	2017-03-20
Structure title title	CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM
Keywords keywords	three-finger toxin fold, antibody Fv fragment, transferase; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.88 Å
Radius of gyration Rg (electron density) rg_electron	19.97 Å
Forward intensity I(0) i0	23695100.00
Molecular weight molecular_weight	35350.0 kDa
Excluded volume excluded_volume	43425 Å³
Envelope volume envelope_volume	51312 Å³
Hydration-shell volume shell_volume	21424 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	26.64 Å
Envelope Rg envelope_rg	20.39 Å
Shape Rg shape_rg	19.94 Å
Total Rg total_rg	20.91 Å
Total atoms total_atoms	2482
Residues n_residues	317
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

▼

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

Maximum dimension Dmax dmax	70.6 Å
Rg (real space) rg_real	20.81 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	2.3700e+07
I(0) uncertainty (real space) i0_real_error	3.4040e+05
Rg (reciprocal space) rg_reciprocal	20.83 Å
I(0) (reciprocal space) i0_reciprocal	23700000.0000
Solution quality estimate total_estimate	0.8037
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.263
Kurtosis Kurtosis kurtosis	-0.330
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5820000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Activin receptor type-2B
Molecular weight formula_weight	11646.9 kDa
EC 编号 ec_number	2.7.11.30
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	2662

GPKAMAETRECIYYNANWELERTNQSGLERCEGEQDKRLHCYASWRNSSGTIELVKKGCWLDDFNCYDRQECVATEENPQVYFCCCEGNFCNERFTHLP

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	anti-human ActRIIB mAb BYM338 heavy-chain
Molecular weight formula_weight	13406.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSYINWVRQAPGQGLEWMGTINPVSGSTSYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGGWFDYWGQGTLVTVSSHHHHHH

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	Escherichia coli

Entity 3 Entity 3 polymer

Description description	anti-human ActRIIB mAb BYM338 light-chain
Molecular weight formula_weight	12496.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

QSALTQPASVSGSPGQSITISCTGTSSDVGSYNYVNWYQQHPGKAPKLMIYGVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCGTFAGGSYYGVFGGGTKLTVLWSHPQFEK

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	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

▼

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5ngva_
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

Domain ID domain_id	d5ngvh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5ngvh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5ngvl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5ngvl2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5ngvA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	5ngvL00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	62.100 Å
Unit-cell length b length_b	114.170 Å
Unit-cell length c length_c	117.940 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	17.050 Å
R factor r_factor	0.1779
R_work r_work	0.1768
R_free r_free	0.1982

fit	/app/data/saxs_computation/ng/5ngv/5ngv.fit
pddf	/app/data/pr_computation/ng/5ngv/5ngv.pr.out
profile	/app/data/saxs_computation/ng/5ngv/5ngv.dat

CRYSTAL STRUCTURE OF THE Activin receptor type-2B LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV, ORTHORHOMBIC CRYSTAL FORM

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

Activin receptor type-2B

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (5 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)