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3g2f

Crystal structure of the kinase domain of bone morphogenetic protein receptor type II (BMPR2) at 2.35 A resolution

Method: X-RAY DIFFRACTION Dmax: 118.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Bone morphogenetic protein receptor type-2

Homo sapiens

UniProt Q13873

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 189–517 Fragment：UNP residues 189-517, protein kinase domain Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.3M ammonium_sulfate, 25% w/v PEG 8000, 0.1M Cacodylate pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.35 Å R-free 0.246
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 189–517 Fragment：UNP residues 189-517, protein kinase domain Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.3M ammonium_sulfate, 25% w/v PEG 8000, 0.1M Cacodylate pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.35 Å R-free 0.246

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 3G2F Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6UNP Crystal structure of the kinase domain of BMPR2-D485G Deposited 2019-10-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 188–529（342 aa） Fragment：kinase domain
Mutation：D485G Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 7 SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1 M Na Cacodylate, pH 6.0, 0.3 M Ammonium sulfate, 22% w/v PEG 8000
Resolution 2.30 Å R-free 0.211
6UNP Crystal structure of the kinase domain of BMPR2-D485G Deposited 2019-10-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 188–529（342 aa） Fragment：kinase domain
Mutation：D485G Non-standard monomer：Yes (specific site not provided by mmCIF) ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 11 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1 M Na Cacodylate, pH 6.0, 0.3 M Ammonium sulfate, 22% w/v PEG 8000
Resolution 2.30 Å R-free 0.211
7PPA High resolution structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 27–150（124 aa）
Chain D 27–150（124 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；294.15 K；14% PEG 3350 0.19 M Ammonium citrate dibasic 0.02 M Sodium citrate tribasic dihydrate
Resolution 1.48 Å R-free 0.207
7PPB 2.4 angstrom crystal structure of bone morphogenetic protein receptor type II (BMPRII) extracellular domain in complex with BMP10 Deposited 2021-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 27–150（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294.15 K；14% PEG 3350 0.14 M KCl
Resolution 2.40 Å R-free 0.235
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13 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 I 27–150（124 aa）
Chain J 27–150（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate
Resolution 3.60 Å R-free 0.282
7PPC Ternary signalling complex of BMP10 bound to ALK1 and BMPRII Deposited 2021-09-13 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 27–150（124 aa）
Chain L 27–150（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294.15 K；20% PEG 3350 0.2 M Calcium acetate hydrate
Resolution 3.60 Å R-free 0.282
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02 Different construct Different mutation/modification 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 27–137（111 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000
Resolution 3.45 Å R-free 0.284
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 27–137（111 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000
Resolution 3.45 Å R-free 0.284
7U5O CRYSTAL STRUCTURE OF THE BONE MORPHOGENETIC PROTEIN RECEPTOR TYPE 2 LIGAND BINDING DOMAIN IN COMPLEX WITH ACTIVIN-B Deposited 2022-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 27–137（111 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；294 K；175 mM Ammonium Sulfate 100 mM Bis Tris 14% PEG 3000
Resolution 3.45 Å R-free 0.284

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BMPR2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–329； UniProt 189–517 Author chain B； PDBConstruct 1–329； UniProt 189–517

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 3g2f

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3g2f
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3g2f
Deposition date deposition_date2009-01-31
Structure title titleCrystal structure of the kinase domain of bone morphogenetic protein receptor type II (BMPR2) at 2.35 A resolution
Keywords keywords;kinase, Structural Genomics, Structural Genomics Consortium, SGC, ATP-binding, Disease mutation, Glycoprotein, Magnesium, Manganese, Membrane, Metal-binding, Nucleotide-binding, Phosphoprotein, Receptor, Serine/threonine-protein kinase, Transferase, Transmembrane ;; 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_guinier31.92 Å
Radius of gyration Rg (electron density) rg_electron32.00 Å
Forward intensity I(0) i088427400.00
Molecular weight molecular_weight71643.0 kDa
Excluded volume excluded_volume88334 ų
Envelope volume envelope_volume112600 ų
Hydration-shell volume shell_volume30743 ų
Envelope diameter envelope_diameter125.6 Å
Shell Rg shell_rg36.70 Å
Envelope Rg envelope_rg32.48 Å
Shape Rg shape_rg32.04 Å
Total Rg total_rg32.28 Å
Total atoms total_atoms4992
Residues n_residues602
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 dmax118.8 Å
Rg (real space) rg_real32.32 Å
Rg uncertainty (real space) rg_real_error1.56 Å
I(0) (real space) i0_real8.8430e+07
I(0) uncertainty (real space) i0_real_error1.6070e+06
Rg (reciprocal space) rg_reciprocal32.15 Å
I(0) (reciprocal space) i0_reciprocal88420000.0000
Solution quality estimate total_estimate0.7702
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.5 Å
Skewness Skewness skewness0.591
Kurtosis Kurtosis kurtosis-0.189
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30370000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.537; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.579; Smooth: 0.817
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3g2fA01
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_id3g2fA02
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_id3g2fB01
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_id3g2fB02
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)