9hdf

Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone

Method: X-RAY DIFFRACTION D_max: 228.6 Å Quality: GOOD

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

Nuclear receptor subfamily 0 group B member 2

OrganismNot specified

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 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
10	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain j； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
11	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain k； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
12	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain l； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
13	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain m； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
14	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain n； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
15	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain o； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 GOL GLYCEROL × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
16	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain p； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain b； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 3 PG4 TETRAETHYLENE GLYCOL × 1 IMD IMIDAZOLE × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain c； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 GOL GLYCEROL × 2 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain d； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain e； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 GOL GLYCEROL × 3 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain f； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CL CHLORIDE ION × 1 IMD IMIDAZOLE × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
7	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain g； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
8	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain h； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244
9	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain i； UniProt 15–29	Not recorded	Ancestral Glucocorticoid Receptor2 ligand binding domain × 1 DEX DEXAMETHASONE × 1 CAC CACODYLATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 IMD IMIDAZOLE × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.085 M sodium cacodylate trihydrate, pH 6.5, 0.17 M ammonium sulfate, 25.5% (w/v) polyethylene glycol 8000 and 15% (v/v) glycerol	Resolution 2.78 Å R-free 0.244

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 9HDF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 15–28（14 aa） Fragment：NR Box1	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 15–28（14 aa） Fragment：NR Box1	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 15–28（14 aa） Fragment：NR Box1 Chain D 15–28（14 aa） Fragment：NR Box1	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
1YUC Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, Bound to Phospholipid and a Fragment of Human SHP Deposited 2005-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 15–28（14 aa） Fragment：NR Box1 Chain D 15–28（14 aa） Fragment：NR Box1	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 1.90 Å R-free 0.248
2Q3Y Ancestral Corticiod Receptor in Complex with DOC Deposited 2007-05-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–27（10 aa） Fragment：hSHP NR Box1	Not recorded	1CA DESOXYCORTICOSTERONE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.240
2Z4J Crystal structure of AR LBD with SHP peptide NR Box 2 Deposited 2007-06-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 115–124（10 aa） Fragment：residues 115-124	Not recorded	DHT 5-ALPHA-DIHYDROTESTOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.1M Bis-Tris Propane, 1.2M Potassium Sodium Tartrate tetrahydrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.60 Å R-free 0.234
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	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 15–28（14 aa） Fragment：UNP residues 15-28 Chain D 15–28（14 aa） Fragment：UNP residues 15-28	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 15–28（14 aa） Fragment：UNP residues 15-28	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4DOR Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human SHP Box1 Deposited 2012-02-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 15–28（14 aa） Fragment：UNP residues 15-28	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；9.5%-15% PEG 3350, 5% glycerol, and 50 mM Bis-Tris, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.220
4ONI Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids Deposited 2014-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 12–30（19 aa） Fragment：NR Box1, UNP residues 12-30	Not recorded	EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；298 K；20-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
4ONI Structure of Human Orphan Receptor LRH1 bound to two bacterial phospholipids Deposited 2014-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 12–30（19 aa） Fragment：NR Box1, UNP residues 12-30	Not recorded	P6L (2S)-3-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6E)-HEXADEC-6-ENOYLOXY]PROPYL (8E)-OCTADEC-8-ENOATE × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；298 K；20-30% PEG 3350, Bis Tris, 5% glycerol, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
6W9M Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with vamorolone and SHP coregulator fragment Deposited 2020-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 17–27（11 aa） Fragment：eleven-residue fragment	Not recorded	TUV vamorolone × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；289.15 K；25% PEG 300 and 0.1 M Tris pH 8.5	Resolution 1.59 Å R-free 0.220
7YXC Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1 PG4 TETRAETHYLENE GLYCOL × 1 CO3 CARBONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；85 mM sodium cacodylate trihydrate, pH 6.5, 0.17 M sodium acetate trihydrate, 25.5% (w/v) PEG8000, 15% (v/v) glycerol	Resolution 2.25 Å R-free 0.245
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXD Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-15	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.30 Å R-free 0.221
7YXN Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.46 Å R-free 0.247
7YXN Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.46 Å R-free 0.247
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1 CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXO Crystal structure of WT AncGR2-LBD bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 17–27（11 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；0.1 M Tris-HCl, pH 8.0, 0.2 M sodium chloride, 2.0 M ammonium sulfate	Resolution 2.99 Å R-free 0.280
7YXR Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.50 Å R-free 0.224
7YXR Crystal structure of mutant AncGR2-LBD (Y545A) bound to dexamethasone and SHP coregulator fragment Deposited 2022-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain S 17–28（12 aa）	Not recorded	DEX DEXAMETHASONE × 1 FMT FORMIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.1 M PIPES, pH 7.0, 0.1 M ammonium acetate, 2.5 M sodium formate	Resolution 2.50 Å R-free 0.224

11 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NR0B2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain a； PDBConstruct 1–15； UniProt 15–29 Author chain b； PDBConstruct 1–15； UniProt 15–29 Author chain c； PDBConstruct 1–15； UniProt 15–29 Author chain d； PDBConstruct 1–15； UniProt 15–29 Author chain e； PDBConstruct 1–15； UniProt 15–29 Author chain f； PDBConstruct 1–15； UniProt 15–29 Author chain g； PDBConstruct 1–15； UniProt 15–29 Author chain h； PDBConstruct 1–15； UniProt 15–29 Author chain i； PDBConstruct 1–15； UniProt 15–29 Author chain j； PDBConstruct 1–15； UniProt 15–29 Author chain k； PDBConstruct 1–15； UniProt 15–29 Author chain l； PDBConstruct 1–15； UniProt 15–29 Author chain m； PDBConstruct 1–15； UniProt 15–29 Author chain n； PDBConstruct 1–15； UniProt 15–29 Author chain o； PDBConstruct 1–15； UniProt 15–29 Author chain p； PDBConstruct 1–15； UniProt 15–29

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9hdf
Deposition date deposition_date	2024-11-12
最后修订 last_revision	2025-11-12
Structure title title	Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone
Keywords keywords	Nuclear Receptor, Glucocorticoid Receptor, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	64.50 Å
Radius of gyration Rg (electron density) rg_electron	64.65 Å
Forward intensity I(0) i0	3081260000.00
Molecular weight molecular_weight	493350.0 kDa
Excluded volume excluded_volume	627150 Å³
Envelope volume envelope_volume	940000 Å³
Hydration-shell volume shell_volume	120280 Å³
Envelope diameter envelope_diameter	216.6 Å
Shell Rg shell_rg	66.57 Å
Envelope Rg envelope_rg	62.53 Å
Shape Rg shape_rg	64.68 Å
Total Rg total_rg	64.61 Å
Total atoms total_atoms	34544
Residues n_residues	4163
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	228.6 Å
Rg (real space) rg_real	64.56 Å
Rg uncertainty (real space) rg_real_error	2.01 Å
I(0) (real space) i0_real	3.0810e+09
I(0) uncertainty (real space) i0_real_error	5.9970e+07
Rg (reciprocal space) rg_reciprocal	64.40 Å
I(0) (reciprocal space) i0_reciprocal	3080000000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	66.7 Å
Skewness Skewness skewness	0.301
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0008
Highest regularization parameter α highest_alpha	146500000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.865

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (14)

Entity 1 Entity 1 polymer

Description description	Ancestral Glucocorticoid Receptor2 ligand binding domain
Molecular weight formula_weight	28649.4 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,F,G,H,I,L,M,P
Atom count atom_count	34585

FPTLISLLEVIEPEVLYSGYDSTLPDTSTRLMSTLNRLGGRQVVSAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYKQSNGNMLCFAPDLVINEERMQLPYMYDQCQQMLKISSEFVRLQVSYDEYLCMKVLLLLSTVPKDGLKSQAVFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEMVGGLLQFCFYTFVNKSLSVEFPEMLAEIISNQLPKFKAGSVKPLLFHQ

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ancestral Glucocorticoid Receptor2 ligand binding domain
Molecular weight formula_weight	28665.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,J,K,N,O

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nuclear receptor subfamily 0 group B member 2
Molecular weight formula_weight	1562.8 kDa
Source method src_method	syn
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p

ASRPAILYALLSSSL

Entity 4 Entity 4 non-polymer

Description description	DEXAMETHASONE
Molecular weight formula_weight	392.5 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 5 Entity 5 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 10 Entity 10 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 12 Entity 12 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 13 Entity 13 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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8. Citations (1)

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Unit-cell length a length_a	264.410 Å
Unit-cell length b length_b	265.464 Å
Unit-cell length c length_c	109.671 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	64

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.780 Å
Low-resolution limit resolution_low	101.570 Å
R factor r_factor	0.2115
R_work r_work	0.2112
R_free r_free	0.2443

fit	/app/data/saxs_computation/hd/9hdf/9hdf.fit
pddf	/app/data/pr_computation/hd/9hdf/9hdf.pr.out
profile	/app/data/saxs_computation/hd/9hdf/9hdf.dat

Glucocorticoid Receptor Ligand Binding Domain in complex with dexamethasone

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

Nuclear receptor subfamily 0 group B member 2

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 (14)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)