SAXSdb — 4asx

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 191–488	Fragment：KINASE DOMAIN, RESIDUES 191-488	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 191–488	Fragment：KINASE DOMAIN, RESIDUES 191-488	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

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 4ASX	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 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 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 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 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
5NH3 CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV Deposited 2017-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 20–135（116 aa）	Not recorded	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
5NH3 CRYSTAL STRUCTURE OF THE Activin receptor type-2A LIGAND BINDING DOMAIN IN COMPLEX WITH BIMAGRUMAB FV Deposited 2017-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–135（116 aa）	Not recorded	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
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 25–322； UniProt 191–488 Author chain B； PDBConstruct 25–322； UniProt 191–488

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	4asx
Deposition date deposition_date	2012-05-03
Structure title title	Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C
Keywords keywords	TRANSFERASE, PROTEIN KINASE; 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	27.11 Å
Radius of gyration Rg (electron density) rg_electron	25.98 Å
Forward intensity I(0) i0	82170500.00
Molecular weight molecular_weight	70427.0 kDa
Excluded volume excluded_volume	87925 Å³
Envelope volume envelope_volume	107990 Å³
Hydration-shell volume shell_volume	33929 Å³
Envelope diameter envelope_diameter	90.0 Å
Shell Rg shell_rg	33.88 Å
Envelope Rg envelope_rg	26.01 Å
Shape Rg shape_rg	25.99 Å
Total Rg total_rg	26.78 Å
Total atoms total_atoms	4942
Residues n_residues	617
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	84.7 Å
Rg (real space) rg_real	26.99 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	8.2170e+07
I(0) uncertainty (real space) i0_real_error	1.1630e+06
Rg (reciprocal space) rg_reciprocal	27.03 Å
I(0) (reciprocal space) i0_reciprocal	82170000.0000
Solution quality estimate total_estimate	0.9064
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.0 Å
Skewness Skewness skewness	0.209
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18370000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.981

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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	ACTIVIN RECEPTOR TYPE-2A
Molecular weight formula_weight	36548.8 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	5328

MGHHHHHHSSGVDLGTENLYFQSMPLQLLEVKARGRFGCVWKAQLLNEYVAVKIFPIQDKQSWQNEYEVYSLPGMKHENILQFIGAEKRGTSVDVDLWLITAFHEKGSLSDFLKANVVSWNELCHIAETMARGLAYLHEDIPGLKDGHKPAISHRDIKSKNVLLKNNLTACIADFGLALKFEAGKSAGDTHGQVGTRRYMAPEVLEGAINFQRDAFLRIDMYAMGLVLWELASRCTAADGPVDEYMLPFEEEIGQHPSLEDMQEVVVHKKKRPVLRDYWQKHAGMAMLCETIEECWDHDAEARLSAGCVGERITQMQRLTNI

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	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 non-polymer

Description description	7,8-bis(chloranyl)-9-methyl-3,4-dihydro-2H-pyrido[3,4-b]indol-1-one
Molecular weight formula_weight	269.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4asxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d4asxa2
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	d4asxb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.0 — automated matches

Domain ID domain_id	d4asxb2
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	4asxA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4asxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	4asxB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	4asxB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	110.426 Å
Unit-cell length b length_b	110.426 Å
Unit-cell length c length_c	208.848 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	24

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1884
R_work r_work	0.1865
R_free r_free	0.2254

fit	/app/data/saxs_computation/as/4asx/4asx.fit
pddf	/app/data/pr_computation/as/4asx/4asx.pr.out
profile	/app/data/saxs_computation/as/4asx/4asx.dat

Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C

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