1zuc

Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist tanaproget

Method: X-RAY DIFFRACTION D_max: 96.0 Å Quality: GOOD

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

Progesterone receptor

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 675–933 Chain B； UniProt 675–933	Not recorded	T98 5-(4,4-DIMETHYL-2-THIOXO-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-6-YL)-1-METHYL-1H-PYRROLE-2-CARBONITRILE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG 3350, MgSO4, PIPES pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.228

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 1ZUC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A28 HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN Deposited 1998-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 2% PEG 4000, 50 MM PIPES PH 6.5, 350 MM LI2SO4, THEN STABILIZED IN THE SAME BUFFER WITH 21% ETHYLENE GLYCOL	Resolution 1.80 Å R-free 0.227
1A28 HORMONE-BOUND HUMAN PROGESTERONE RECEPTOR LIGAND-BINDING DOMAIN Deposited 1998-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 2% PEG 4000, 50 MM PIPES PH 6.5, 350 MM LI2SO4, THEN STABILIZED IN THE SAME BUFFER WITH 21% ETHYLENE GLYCOL	Resolution 1.80 Å R-free 0.227
1E3K Human Progesteron Receptor Ligand Binding Domain in complex with the ligand metribolone (R1881) Deposited 2000-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 676–933（258 aa） Fragment：LIGAND-BINDING DOMAIN	Not recorded	R18 (17BETA)-17-HYDROXY-17-METHYLESTRA-4,9,11-TRIEN-3-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；RESERVOIR SOLUTION: 10% ISO-PROPANOL, 100MM SODIUM CITRATE 50MM HEPES PH 7.5. THE DROPS WERE SET UP USING THE HANGING DROP METHOD AND WERE COMPOSED OF A 2:1 RATIO OF PROTEIN AND RESERVOIR SOLUTIONS.	Resolution 2.80 Å R-free 0.343
1E3K Human Progesteron Receptor Ligand Binding Domain in complex with the ligand metribolone (R1881) Deposited 2000-06-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 676–933（258 aa） Fragment：LIGAND-BINDING DOMAIN	Not recorded	R18 (17BETA)-17-HYDROXY-17-METHYLESTRA-4,9,11-TRIEN-3-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；RESERVOIR SOLUTION: 10% ISO-PROPANOL, 100MM SODIUM CITRATE 50MM HEPES PH 7.5. THE DROPS WERE SET UP USING THE HANGING DROP METHOD AND WERE COMPOSED OF A 2:1 RATIO OF PROTEIN AND RESERVOIR SOLUTIONS.	Resolution 2.80 Å R-free 0.343
1SQN Progesterone Receptor Ligand Binding Domain with bound Norethindrone Deposited 2004-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 673–933（261 aa） Fragment：residues 676-933, ligand binding domain	Not recorded	NDR (14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 1000, Li2SO4. hepes pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.45 Å R-free 0.216
1SQN Progesterone Receptor Ligand Binding Domain with bound Norethindrone Deposited 2004-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 673–933（261 aa） Fragment：residues 676-933, ligand binding domain	Not recorded	NDR (14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG 1000, Li2SO4. hepes pH 6.5, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 22K	Resolution 1.45 Å R-free 0.216
1SR7 Progesterone Receptor Hormone Binding Domain with Bound Mometasone Furoate Deposited 2004-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 676–933（258 aa） Fragment：Ligand binding domain Chain B 676–933（258 aa） Fragment：Ligand binding domain	Not recorded	MOF MOMETASONE FUROATE × 2 SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；PEG 1000, Li2SO4, hepes, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.46 Å R-free 0.211
2C7A STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX Deposited 2005-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 399–476（78 aa） Fragment：DNA BINDING DOMAIN, RESIDUES 399-476 Chain B 399–476（78 aa） Fragment：DNA BINDING DOMAIN, RESIDUES 399-476	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.246
2OVH Progesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor SMRT Deposited 2007-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 678–933（256 aa） Fragment：PR LBD	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1M Tris, 0.4M NaCl, 10% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.222
2OVH Progesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor SMRT Deposited 2007-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 678–933（256 aa） Fragment：PR LBD	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1M Tris, 0.4M NaCl, 10% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.222
2OVM Progesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor NCoR Deposited 2007-02-14	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 A 678–933（256 aa） Fragment：Ligand Binding Domain (residues 678-933)	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；0.1M Tris, 0.15M NaCl, 10% glycerol, pH 8.0, spontaneous crystallization, temperature 277K	Resolution 2.60 Å R-free 0.244
2OVM Progesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor NCoR Deposited 2007-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 678–933（256 aa） Fragment：Ligand Binding Domain (residues 678-933)	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；277 K；0.1M Tris, 0.15M NaCl, 10% glycerol, pH 8.0, spontaneous crystallization, temperature 277K	Resolution 2.60 Å R-free 0.244
2W8Y RU486 bound to the progesterone receptor in a destabilized agonistic conformation Deposited 2009-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 678–933（256 aa） Fragment：PR LBD, RESIDUES 678-933	Not recorded	486 11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22.5% PEG4000, 0.1M HEPES 6.5, 100 MM LI2SO4	Resolution 1.80 Å R-free 0.218
2W8Y RU486 bound to the progesterone receptor in a destabilized agonistic conformation Deposited 2009-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 678–933（256 aa） Fragment：PR LBD, RESIDUES 678-933	Not recorded	NDR (14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；22.5% PEG4000, 0.1M HEPES 6.5, 100 MM LI2SO4	Resolution 1.80 Å R-free 0.218
3D90 Crystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel Deposited 2008-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 676–933（258 aa） Fragment：Ligand-binding domain, UNP residues 676-933	Not recorded	NOG 13-BETA-ETHYL-17-ALPHA-ETHYNYL-17-BETA-HYDROXYGON-4-EN-3-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG3350, x300mM MgSO4, 10% Glycerol 10%, 50mM PIPES, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.279
3D90 Crystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel Deposited 2008-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 676–933（258 aa） Fragment：Ligand-binding domain, UNP residues 676-933	Not recorded	NOG 13-BETA-ETHYL-17-ALPHA-ETHYNYL-17-BETA-HYDROXYGON-4-EN-3-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；8% PEG3350, x300mM MgSO4, 10% Glycerol 10%, 50mM PIPES, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.26 Å R-free 0.279
3G8O Progesterone Receptor with bound Pyrrolidine 1 Deposited 2009-02-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 673–933（261 aa） Fragment：ligand binding domain Chain B 673–933（261 aa） Fragment：ligand binding domain	Not recorded	30X N~2~-[4-cyano-3-(trifluoromethyl)phenyl]-N,N-dimethyl-N~2~-(2,2,2-trifluoroethyl)-L-alaninamide × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 7；298 K；0.1M Hepes, 0.2M Lithium Sulfate, 15% PEG3350, pH 7.0, hanging drop, temperature 298K	Resolution 1.90 Å R-free 0.241
3HQ5 Progesterone Receptor bound to an Alkylpyrrolidine ligand. Deposited 2009-06-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 678–933（256 aa） Fragment：residues 678-933 Chain B 678–933（256 aa） Fragment：residues 678-933	Not recorded	SO4 SULFATE ION × 4 GKK 2-chloro-4-{[(3S)-1-methylpyrrolidin-3-yl][2-(trifluoromethyl)benzyl]amino}benzonitrile × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；20 % Peg 3350, 0.2M LiSO4, 0.1M Hepes 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K	Resolution 2.10 Å R-free 0.237
3KBA Progesterone receptor bound to sulfonamide pyrrolidine partial agonist Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 681–933（253 aa） Fragment：Steroid-binding region: UNP residues 681-933	Not recorded	WOW 2-chloro-4-{(2-methylbenzyl)[(3S)-1-(methylsulfonyl)pyrrolidin-3-yl]amino}benzonitrile × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 2mM Li2SO4, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.250
3KBA Progesterone receptor bound to sulfonamide pyrrolidine partial agonist Deposited 2009-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 681–933（253 aa） Fragment：Steroid-binding region: UNP residues 681-933	Not recorded	WOW 2-chloro-4-{(2-methylbenzyl)[(3S)-1-(methylsulfonyl)pyrrolidin-3-yl]amino}benzonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 2mM Li2SO4, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.250
3ZR7 Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES	Not recorded	OR8 2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE × 1 GOL GLYCEROL × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30%POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.65 Å R-free 0.192
3ZR7 Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES	Not recorded	OR8 2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30%POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.65 Å R-free 0.192
3ZRA Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 678–933（256 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 678-933	Not recorded	ORB N-{(1R)-1-[4-(2-CHLORO-5-FLUOROPYRIDIN-3-YL)PHENYL]ETHYL}-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL.	Resolution 1.90 Å R-free 0.248
3ZRA Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 678–933（256 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 678-933	Not recorded	ORB N-{(1R)-1-[4-(2-CHLORO-5-FLUOROPYRIDIN-3-YL)PHENYL]ETHYL}-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL.	Resolution 1.90 Å R-free 0.248
3ZRB Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 678-933	Not recorded	OR8 2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE × 1 SO4 SULFATE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30%POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.80 Å R-free 0.221
3ZRB Structural basis for agonism and antagonism for a set of chemically related progesterone receptor modulators Deposited 2011-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 678–933（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 678-933	Not recorded	GOL GLYCEROL × 1 ORC (R)-N-[1-[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]ETHYL]-3,5-DIMETHYLISOXAZOLE-4-SULFONAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30%POLYETHYLENE GLYCOL 3350, 0.1M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.80 Å R-free 0.221
4A2J PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids Deposited 2011-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 514–769（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 514-769	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL.	Resolution 2.00 Å R-free 0.251
4A2J PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids Deposited 2011-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 514–769（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 514-769	Not recorded	AS0 4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL.	Resolution 2.00 Å R-free 0.251
4APU PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids Deposited 2012-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 514–769（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 514-769	Not recorded	OR8 2-CHLORO-N-[[4-(3,5-DIMETHYLISOXAZOL-4-YL)PHENYL]METHYL]-1,4-DIMETHYL-1H-PYRAZOLE-4-SULFONAMIDE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.90 Å R-free 0.252
4APU PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids Deposited 2012-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 514–769（256 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 514-769	Not recorded	A2K (8S,11R,13S,14S,16S,17S)-17-cyclopropylcarbonyl-16-ethenyl-13-methyl-11-(4-pyridin-3-ylphenyl)-2,6,7,8,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；20-30% POLYETHYLENE GLYCOL 3350, 0.1 M HEPES PH 6.5, 100 MM MG2SO4, 10% GLYCEROL	Resolution 1.90 Å R-free 0.252
4OAR Progesterone receptor with bound ulipristal acetate and a peptide from the co-repressor SMRT Deposited 2014-01-06	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 A 678–933（256 aa） Fragment：Steroid-binding Region	Not recorded	2S0 [(8S,11R,13S,14S,17R)-17-acetyl-11-[4-(dimethylamino)phenyl]-13-methyl-3-oxo-1,2,6,7,8,11,12,14,15,16-decahydrocyclopen ta[a]phenanthren-17-yl] acetate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% PEG3350, Tris,HCl 50mM, NaCl 400mM, 10% Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.234

18 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRGR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–259； UniProt 675–933 Author chain B； PDBConstruct 1–259； UniProt 675–933

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	1zuc
Deposition date deposition_date	2005-05-30
Structure title title	Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist tanaproget
Keywords keywords	progesterone receptor, nonsteroidal agonist, tanaproget, progesterone, hormone, HORMONE-GROWTH FACTOR COMPLEX; HORMONE/GROWTH FACTOR
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	27.62 Å
Radius of gyration Rg (electron density) rg_electron	26.73 Å
Forward intensity I(0) i0	50960600.00
Molecular weight molecular_weight	58625.0 kDa
Excluded volume excluded_volume	74758 Å³
Envelope volume envelope_volume	90070 Å³
Hydration-shell volume shell_volume	28442 Å³
Envelope diameter envelope_diameter	103.0 Å
Shell Rg shell_rg	33.51 Å
Envelope Rg envelope_rg	26.82 Å
Shape Rg shape_rg	26.72 Å
Total Rg total_rg	27.53 Å
Total atoms total_atoms	4117
Residues n_residues	502
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	96.0 Å
Rg (real space) rg_real	27.64 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	5.0960e+07
I(0) uncertainty (real space) i0_real_error	6.8350e+05
Rg (reciprocal space) rg_reciprocal	27.64 Å
I(0) (reciprocal space) i0_reciprocal	50960000.0000
Solution quality estimate total_estimate	0.7953
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.557
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14150000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Progesterone receptor
Molecular weight formula_weight	29795.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	4296

GSPGQDIQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLLFHKK

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 BL21

Entity 2 Entity 2 non-polymer

Description description	5-(4,4-DIMETHYL-2-THIOXO-1,4-DIHYDRO-2H-3,1-BENZOXAZIN-6-YL)-1-METHYL-1H-PYRROLE-2-CARBONITRILE
Molecular weight formula_weight	297.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zuca_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

Domain ID domain_id	d1zucb_
Class class	a — All alpha proteins
Fold Fold fold	a.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamily	a.123.1 — Nuclear receptor ligand-binding domain
Family Family family	a.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1zucA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

Domain ID domain_id	1zucB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	565 — Retinoid X Receptor
Homologous superfamily homologous superfamily	10 — Retinoid X Receptor

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8. Citations (1)

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Unit-cell length a length_a	57.519 Å
Unit-cell length b length_b	64.497 Å
Unit-cell length c length_c	70.406 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1812
R_work r_work	0.1788
R_free r_free	0.2281

fit	/app/data/saxs_computation/zu/1zuc/1zuc.fit
pddf	/app/data/pr_computation/zu/1zuc/1zuc.pr.out
profile	/app/data/saxs_computation/zu/1zuc/1zuc.dat