SAXSdb — 3qb4

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

Growth/differentiation factor 5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 387–501	Fragment：GDF-5, residues 387-501 Mutation：R57A	Bone morphogenetic protein receptor type-1A × 1 （P36894）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 387–501	Fragment：GDF-5, residues 387-501 Mutation：R57A	Bone morphogenetic protein receptor type-1A × 1 （P36894）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 387–501 Chain C； UniProt 387–501	Fragment：GDF-5, residues 387-501 Mutation：R57A	Bone morphogenetic protein receptor type-1A × 2 （P36894）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241

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 3QB4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WAQ Crystal structure of human Growth and Differentiation Factor 5 (GDF-5) Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 387–501（115 aa） Fragment：RESIDUES 387-501 (RESIDUES 6-120 OF MATURE GDF-5)	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 25% 2-METHLY-2,4-PENTANEDIOL, 0.1M SODIUM CITRATE PH 4.0	Resolution 2.28 Å R-free 0.237
2BHK Crystal structure of human growth and differentiation factor 5 (GDF5) Deposited 2005-01-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 382–501（120 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；100 MM SODIUM ACETATE, PH 5.0 30% ISOPROPANOL 14 MG/ML PROTEIN HANGING DROP	Resolution 2.40 Å R-free 0.220
3EVS Crystal structure of the GDF-5:BMP receptor IB complex. Deposited 2008-10-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 387–501（115 aa） Fragment：UNP residues 387-501	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.25；294 K；0.1M sodium acetate, 50% PPG 400, 30mM magnesium sulfate, pH 5.25, VAPOR DIFFUSION, temperature 294K	Resolution 2.10 Å R-free 0.256
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain C 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain C 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 382–501（120 aa） Chain D 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
5HK5 Structure of the Grem2-GDF5 Inhibitory Complex Deposited 2016-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 382–501（120 aa） Chain D 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES, ammonium chloride, ethylammonium nitrate	Resolution 2.90 Å R-free 0.282
6Z3G Repulsive Guidance Molecule A (RGMA) in complex with Growth Differentiation Factor 5 (GDF5) Deposited 2020-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 aa）	Not recorded	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.5, 24% v/v polyethylene glycol (PEG) 400.	Resolution 2.78 Å R-free 0.288
6Z3H Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 2) Deposited 2020-05-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M (NH4)2SO4, 0.1 M sodium acetate pH 4.6, 35% w/v pentaerythritol ethoxylate (15/4 EO/OH; average MW 797 Da)	Resolution 3.16 Å R-free 0.268
6Z3J Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) (crystal form 1) Deposited 2020-05-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 aa） Chain B 387–501（115 aa）	Mutation：Y487K, Q489D Mutation：Y487K, Q489D	SO4 SULFATE ION × 2 GOL GLYCEROL × 2 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；294 K；0.2 M Li2SO4, 0.1 M HEPES pH 7.5, 25% v/v PEG 3350.	Resolution 1.65 Å R-free 0.219
6Z3L Repulsive Guidance Molecule C (RGMC, Hemojuvelin, HJV, HFE2) in complex with Growth Differentiation Factor 5 (GDF5) Deposited 2020-05-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 387–501（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；1 M LiCl, 0.1 M citric acid pH 4.0, 8% gamma-butyrolactone.	Resolution 2.51 Å R-free 0.267
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 387–501（115 aa） Chain B 387–501（115 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain G 387–501（115 aa） Chain H 387–501（115 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428
6Z3M Repulsive Guidance Molecule B (RGMB) in complex with Growth Differentiation Factor 5 (GDF5) and Neogenin 1 (NEO1). Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain M 387–501（115 aa） Chain N 387–501（115 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；0.1 M NaCl, 20 mM MES pH 6.7, 6.6% w/v PEG 4000	Resolution 5.50 Å R-free 0.428
7ZJF R399E, a mutated form of GDF5, for disease modification of osteoarthritis Deposited 2022-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.15；293 K；01 M Hepes, 32% PEG 400, 230 mM MgCl2, pH 8.15	Resolution 1.30 Å R-free 0.222
8BWL Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium Deposited 2022-12-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 1.96 Å R-free 0.212
8BWM Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4042 eV) Deposited 2022-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；12.1% w/v PEG 1000, 12.1% w/v PEG 3350, 12.1% v/v MPD, 97 mM CaCl2, 0.097 M Bicine/Trizma pH 8.5	Resolution 2.50 Å R-free 0.278
8BWN Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation Factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4010 eV) Deposited 2022-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 382–501（120 aa） Chain B 382–501（120 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 100 mM CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 2.57 Å R-free 0.283
8E3G BMP2/GDF5 heterodimer Deposited 2022-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 382–501（120 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, magnesium formate	Resolution 2.80 Å R-free 0.234
8E3G BMP2/GDF5 heterodimer Deposited 2022-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 382–501（120 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris, magnesium formate	Resolution 2.80 Å R-free 0.234

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GDF5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–117； UniProt 387–501 Author chain C； PDBConstruct 3–117； UniProt 387–501

Bone morphogenetic protein receptor type-1A

Homo sapiens

UniProt P36894

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 24–152	Fragment：BMP receptor BMPR-IA, residues 24-152	Growth/differentiation factor 5 × 1 （P43026）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 24–152	Fragment：BMP receptor BMPR-IA, residues 24-152	Growth/differentiation factor 5 × 1 （P43026）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 24–152 Chain D； UniProt 24–152	Fragment：BMP receptor BMPR-IA, residues 24-152	Growth/differentiation factor 5 × 2 （P43026）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Hepes pH 7.5, 0.2M NaCl 20% (w/v) PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.28 Å R-free 0.241

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 3QB4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ES7 COMPLEX BETWEEN BMP-2 AND TWO BMP RECEPTOR IA ECTODOMAINS Deposited 2000-04-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 55–143（89 aa） Fragment：EXTRACELLULAR DOMAIN Chain D 55–143（89 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；sodium acetate, imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.90 Å R-free 0.229
1REW Structural refinement of the complex of bone morphogenetic protein 2 and its type IA receptor Deposited 2003-11-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–152（129 aa） Fragment：extracellular domain Chain D 24–152（129 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；280 K；sodium acetate, imidazole, glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K	Resolution 1.86 Å R-free 0.229
2GOO Ternary Complex of BMP-2 bound to BMPR-Ia-ECD and ActRII-ECD Deposited 2006-04-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 24–152（129 aa） Fragment：Residues 24-152 Chain E 24–152（129 aa） Fragment：Residues 24-152	Not recorded	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；4M sodium formate, 100mM Hepes, 3% dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.259
2H62 Crystal structure of a ternary ligand-receptor complex of BMP-2 Deposited 2006-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–152（129 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.75；294 K；50% PPG400, 0.1M Bis-Tris, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.85 Å R-free 0.225
2H64 Crystal structure of a ternary ligand-receptor complex of BMP-2 Deposited 2006-05-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 24–152（129 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.75；294 K；30% PEG3350, 0.1M Tris-HCl pH 8.75, 0.2M NH4CH3COO, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.92 Å R-free 0.264
2K3G NMR structure analysis of a BMP receptor Deposited 2008-05-07	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 51–152（102 aa） Fragment：Extracellular domain (UNP residues 51-152)	Mutation：A28G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Pressure ambient NMR sample composition 1.1 mM [U-99% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-94% 13C; U-98% 15N] Bone Morphogenetic Protein Receptor Type IA, 10 mM potassium phosphate, 0.2 w/v sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2QJ9 Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B1 Deposited 2007-07-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–152（129 aa） Fragment：extracellular domain (residues 24-152) Chain D 24–152（129 aa） Fragment：extracellular domain (residues 24-152)	Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.44 Å R-free 0.253
2QJA Crystal structure analysis of BMP-2 in complex with BMPR-IA variant B12 Deposited 2007-07-06	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–152（129 aa） Fragment：extracellular domain (residues 24-152) Chain D 24–152（129 aa） Fragment：extracellular domain (residues 24-152)	Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.254
2QJB Crystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB Deposited 2007-07-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–152（129 aa） Fragment：extracellular domain (residues 24-152) Chain D 24–152（129 aa） Fragment：extracellular domain (residues 24-152)	Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L,D46E,G42H,A61T,I62M Mutation：K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L,D46E,G42H,A61T,I62M	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.263
3NH7 Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA Deposited 2010-06-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 24–152（129 aa） Fragment：extracellular domain, UNP residues 24-152	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.280
3NH7 Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA Deposited 2010-06-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–152（129 aa） Fragment：extracellular domain, UNP residues 24-152	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.280
3NH7 Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA Deposited 2010-06-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 24–152（129 aa） Fragment：extracellular domain, UNP residues 24-152	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.280
3NH7 Crystal structure of the neutralizing Fab fragment AbD1556 bound to the BMP type I receptor IA Deposited 2010-06-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 24–152（129 aa） Fragment：extracellular domain, UNP residues 24-152	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；100mM Tris-HCl pH 7.0, 20% (w/v) PEG 8000 and 10% (w/v) glucose , VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.70 Å R-free 0.280

10 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BMR1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–135； UniProt 24–152 Author chain D； PDBConstruct 7–135； UniProt 24–152

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	3qb4
Deposition date deposition_date	2011-01-12
Structure title title	Crystal structure of a TGF-beta ligand-receptor complex
Keywords keywords	CYSTINE-KNOT, Ligand-receptor complex, Protein, Membrane/Extracellular, CYTOKINE-TRANSFERASE RECEPTOR complex; CYTOKINE/TRANSFERASE RECEPTOR
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	24.01 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	35319300.00
Molecular weight molecular_weight	43356.0 kDa
Excluded volume excluded_volume	53188 Å³
Envelope volume envelope_volume	66136 Å³
Hydration-shell volume shell_volume	23571 Å³
Envelope diameter envelope_diameter	79.9 Å
Shell Rg shell_rg	30.23 Å
Envelope Rg envelope_rg	23.90 Å
Shape Rg shape_rg	23.72 Å
Total Rg total_rg	24.30 Å
Total atoms total_atoms	3015
Residues n_residues	388
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	77.5 Å
Rg (real space) rg_real	24.03 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	3.5320e+07
I(0) uncertainty (real space) i0_real_error	4.5620e+05
Rg (reciprocal space) rg_reciprocal	24.03 Å
I(0) (reciprocal space) i0_reciprocal	35320000.0000
Solution quality estimate total_estimate	0.8936
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.4 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.462
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5673000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Growth/differentiation factor 5
Molecular weight formula_weight	13319.4 kDa
Mutation mutation	R57A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3108

MKRQGKRPSKNLKARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLASHLEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGCR

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Bone morphogenetic protein receptor type-1A
Molecular weight formula_weight	14674.5 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	B,D

GSGAMAQNLDSMLHGTGMKSDSDQKKSENGVTLAPEDTLPFLKCYCSGHCPDDAINNTCITNGHCFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPPVVIGPFFDGSIR

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	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3qb4a_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d3qb4b_
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	d3qb4c_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.0 — automated matches

Domain ID domain_id	d3qb4d_
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

CATH v4.4 (4 domains)

Domain ID domain_id	3qb4A00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3qb4B00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

Domain ID domain_id	3qb4C00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

Domain ID domain_id	3qb4D00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	60 — CD59
Homologous superfamily homologous superfamily	10 — CD59

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8. Citations (1)

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Unit-cell length a length_a	63.810 Å
Unit-cell length b length_b	62.850 Å
Unit-cell length c length_c	124.991 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.85 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	24.000 Å
R factor r_factor	0.1998
R_work r_work	0.1975
R_free r_free	0.2414

fit	/app/data/saxs_computation/qb/3qb4/3qb4.fit
pddf	/app/data/pr_computation/qb/3qb4/3qb4.pr.out
profile	/app/data/saxs_computation/qb/3qb4/3qb4.dat

Crystal structure of a TGF-beta ligand-receptor complex

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

Growth/differentiation factor 5

State in the Current Structure

Other States of the Same Protein in the Database

Bone morphogenetic protein receptor type-1A

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)