SAXSdb — 5nh3

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

Activin receptor type-2A

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 20–135	Not recorded	anti-human ActRIIB mAb BYM338 Fv heavy-chain × 1 anti-human ActRIIB mAb BYM338 Fv light-chain × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium citrate tribasic dihydrate pH3.5 25% PEG 3350	Resolution 2.35 Å R-free 0.208
2	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 20–135	Not recorded	anti-human ActRIIB mAb BYM338 Fv heavy-chain × 1 anti-human ActRIIB mAb BYM338 Fv light-chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium citrate tribasic dihydrate pH3.5 25% PEG 3350	Resolution 2.35 Å R-free 0.208

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 5NH3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3Q4T Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin Deposited 2010-12-24	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 191–488（298 aa） Fragment：kinase domain (UNP residues 191-488)	Not recorded	TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 10 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293.15 K；28% PEG 3350, 0.2M LiSO4, 0.1M Tris, pH 8.8, 10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.96 Å R-free 0.223
3Q4T Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin Deposited 2010-12-24	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 191–488（298 aa） Fragment：kinase domain (UNP residues 191-488)	Not recorded	TAK 6-[4-(2-piperidin-1-ylethoxy)phenyl]-3-pyridin-4-ylpyrazolo[1,5-a]pyrimidine × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.8；293.15 K；28% PEG 3350, 0.2M LiSO4, 0.1M Tris, pH 8.8, 10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.96 Å R-free 0.223
3SOC Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin Deposited 2011-06-30	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 191–488（298 aa） Fragment：kinase domain (residue 191-488)	Not recorded	GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；20% PEG 3350, 0.1M Tris, pH 8.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.95 Å R-free 0.211
3SOC Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin Deposited 2011-06-30	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 191–488（298 aa） Fragment：kinase domain (residue 191-488)	Not recorded	GVD [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；20% PEG 3350, 0.1M Tris, pH 8.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K	Resolution 1.95 Å R-free 0.211
4ASX Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C Deposited 2012-05-03	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 191–488（298 aa） Fragment：KINASE DOMAIN, RESIDUES 191-488	Not recorded	6OJ 7,8-bis(chloranyl)-9-methyl-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 3350 0.20 M NA(MALONATE)	Resolution 2.05 Å R-free 0.225
4ASX Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C Deposited 2012-05-03	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 191–488（298 aa） Fragment：KINASE DOMAIN, RESIDUES 191-488	Not recorded	6OJ 7,8-bis(chloranyl)-9-methyl-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions 20 % PEG 3350 0.20 M NA(MALONATE)	Resolution 2.05 Å R-free 0.225
7U5P CRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-A Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294 K；100mM Sodium Citrate, 17%PEG 3000	Resolution 3.14 Å R-free 0.276
7U5P CRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-A Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–121（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294 K；100mM Sodium Citrate, 17%PEG 3000	Resolution 3.14 Å R-free 0.276
7U5P CRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-A Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–121（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294 K；100mM Sodium Citrate, 17%PEG 3000	Resolution 3.14 Å R-free 0.276
7U5P CRYSTAL STRUCTURE OF THE ACTIVIN RECEPTOR TYPE-2A LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-A Deposited 2022-03-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–121（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294 K；100mM Sodium Citrate, 17%PEG 3000	Resolution 3.14 Å R-free 0.276

4 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AVR2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 20–135 Author chain B； PDBConstruct 1–116； UniProt 20–135

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	5nh3
Deposition date deposition_date	2017-03-21
Structure title title	CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV
Keywords keywords	OTHER, EPITOPE MAPPING, transferase; TRANSFERASE
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	31.78 Å
Radius of gyration Rg (electron density) rg_electron	31.64 Å
Forward intensity I(0) i0	83884300.00
Molecular weight molecular_weight	69807.0 kDa
Excluded volume excluded_volume	85989 Å³
Envelope volume envelope_volume	111410 Å³
Hydration-shell volume shell_volume	30691 Å³
Envelope diameter envelope_diameter	119.5 Å
Shell Rg shell_rg	36.87 Å
Envelope Rg envelope_rg	31.30 Å
Shape Rg shape_rg	31.62 Å
Total Rg total_rg	32.12 Å
Total atoms total_atoms	4902
Residues n_residues	637
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	112.0 Å
Rg (real space) rg_real	32.00 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	8.3880e+07
I(0) uncertainty (real space) i0_real_error	1.4240e+06
Rg (reciprocal space) rg_reciprocal	31.91 Å
I(0) (reciprocal space) i0_reciprocal	83880000.0000
Solution quality estimate total_estimate	0.8549
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.448
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8925000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.813; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Activin receptor type-2A
Molecular weight formula_weight	14196.8 kDa
EC 编号 ec_number	2.7.11.30
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	5263

AILGRSETQECLFFNANWEKDRTNQTGVEPCYGDKDKRRHCFATWKNISGSIEIVKQGCWLDDINCYDRTDCVEKKDSPEVYFCCCEGNMCNEKFSYFPEMEVTQPTSNPVTPKPPEFRHDS

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	anti-human ActRIIB mAb BYM338 Fv heavy-chain
Molecular weight formula_weight	13406.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I

QVQLVQSGAEVKKPGASVKVSCKASGYTFTSSYINWVRQAPGQGLEWMGTINPVSGSTSYAQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARGGWFDYWGQGTLVTVSSHHHHHH

Entity 3 Entity 3 polymer

Description description	anti-human ActRIIB mAb BYM338 Fv light-chain
Molecular weight formula_weight	12513.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

QSALTQPASVSGSPGQSITISCTGTSSDVGSYNYVNWYQQHPGKAPKLMIYGVSKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCGTFAGGSYYGVFGGGTKLTVLWSHPQFEK

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 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	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	361

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7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5nh3a_
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	d5nh3b_
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	d5nh3h1
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	d5nh3h2
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	d5nh3i1
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	d5nh3i2
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	d5nh3l1
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	d5nh3l2
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	d5nh3m1
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	d5nh3m2
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 (4 domains)

Domain ID domain_id	5nh3A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	5nh3B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	5nh3L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5nh3M00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	44.330 Å
Unit-cell length b length_b	108.207 Å
Unit-cell length c length_c	100.685 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	47.550 Å
R factor r_factor	0.1679
R_work r_work	0.1658
R_free r_free	0.2083

fit	/app/data/saxs_computation/nh/5nh3/5nh3.fit
pddf	/app/data/pr_computation/nh/5nh3/5nh3.pr.out
profile	/app/data/saxs_computation/nh/5nh3/5nh3.dat

CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV

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

Activin receptor type-2A

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (10 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)