← Back to search
3q4t

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

Method: X-RAY DIFFRACTION Dmax: 82.7 Å Quality: EXCELLENT
▼

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

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 3Q4T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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
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 3q4t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3q4t
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3q4t
Deposition date deposition_date2010-12-24
Structure title titleCrystal structure of Activin receptor type-IIA (ACVR2A) kinase domain in complex with dorsomorphin
Keywords keywordsStructural Genomics Consortium, SGC, Protein kinase, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier27.02 Å
Radius of gyration Rg (electron density) rg_electron25.91 Å
Forward intensity I(0) i085387600.00
Molecular weight molecular_weight71801.0 kDa
Excluded volume excluded_volume89644 ų
Envelope volume envelope_volume108460 ų
Hydration-shell volume shell_volume34191 ų
Envelope diameter envelope_diameter87.5 Å
Shell Rg shell_rg33.93 Å
Envelope Rg envelope_rg25.94 Å
Shape Rg shape_rg25.91 Å
Total Rg total_rg26.75 Å
Total atoms total_atoms5034
Residues n_residues613
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
▼

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

Maximum dimension Dmax dmax82.7 Å
Rg (real space) rg_real26.90 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real8.5390e+07
I(0) uncertainty (real space) i0_real_error1.2010e+06
Rg (reciprocal space) rg_reciprocal26.94 Å
I(0) (reciprocal space) i0_reciprocal85390000.0000
Solution quality estimate total_estimate0.9104
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.2 Å
Skewness Skewness skewness0.207
Kurtosis Kurtosis kurtosis-0.487
Angular range angular_range— – 0.2950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18260000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.978
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3q4ta1
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_idd3q4ta2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3q4tb1
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_idd3q4tb2
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_id3q4tA01
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_id3q4tA02
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_id3q4tB01
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_id3q4tB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
▶

8. Citations (1)

▶

9. Files and Curves (10)