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3soc

Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin

Method: X-RAY DIFFRACTION Dmax: 83.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Activin receptor type-2A

Homo sapiens

UniProt P27037

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 (residue 191-488) 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 191–488 Fragment：kinase domain (residue 191-488) 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

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 3SOC 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
4ASX Crystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dihydro-Bauerine C Deposited 2012-05-03 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, 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 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
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.

SAXS scattering curve SAXS Profile

SAXS profile for 3soc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3soc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3soc
Deposition date deposition_date2011-06-30
Structure title titleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with a quinazolin
Keywords keywordsStructural Genomics Consortium, SGC, TRANSFERASE, Protein kinase; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.10 Å
Radius of gyration Rg (electron density) rg_electron25.99 Å
Forward intensity I(0) i082117300.00
Molecular weight molecular_weight70704.0 kDa
Excluded volume excluded_volume88373 ų
Envelope volume envelope_volume107750 ų
Hydration-shell volume shell_volume33797 ų
Envelope diameter envelope_diameter88.9 Å
Shell Rg shell_rg33.94 Å
Envelope Rg envelope_rg26.04 Å
Shape Rg shape_rg25.99 Å
Total Rg total_rg26.82 Å
Total atoms total_atoms4969
Residues n_residues616
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax83.7 Å
Rg (real space) rg_real26.98 Å
Rg uncertainty (real space) rg_real_error0.47 Å
I(0) (real space) i0_real8.2120e+07
I(0) uncertainty (real space) i0_real_error1.0970e+06
Rg (reciprocal space) rg_reciprocal27.02 Å
I(0) (reciprocal space) i0_reciprocal82120000.0000
Solution quality estimate total_estimate0.8881
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.6 Å
Skewness Skewness skewness0.208
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17480000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.711
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3soca1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd3soca2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3socb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.0 — automated matches
Domain ID domain_idd3socb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id3socA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3socA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id3socB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3socB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)