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3d90

Crystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel

Method: X-RAY DIFFRACTION Dmax: 86.6 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Progesterone receptor

Homo sapiens

UniProt P06401

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 676–933 Fragment：Ligand-binding domain, UNP residues 676-933 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 676–933 Fragment：Ligand-binding domain, UNP residues 676-933 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

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 3D90 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 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 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 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 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 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 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 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 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
1ZUC Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist tanaproget Deposited 2005-05-30 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 675–933（259 aa）
Chain B 675–933（259 aa）
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
2C7A STRUCTURE OF THE PROGESTERONE RECEPTOR-DNA COMPLEX Deposited 2005-11-19 Different construct Different mutation/modification 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 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 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 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 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 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 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
3G8O Progesterone Receptor with bound Pyrrolidine 1 Deposited 2009-02-12 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 30 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 1–258； UniProt 676–933 Author chain B； PDBConstruct 1–258； UniProt 676–933

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

SAXS profile for 3d90

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3d90
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3d90
Deposition date deposition_date2008-05-26
Structure title titleCrystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel
Keywords keywords;progesterone receptor, steroid receptor, nuclear receptor, transcription factor, women health, contraception, Alternative splicing, DNA-binding, Lipid-binding, Metal-binding, Nucleus, Phosphoprotein, Polymorphism, Receptor, Steroid-binding, Transcription, Transcription regulation, Zinc, Zinc-finger ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.50 Å
Radius of gyration Rg (electron density) rg_electron26.47 Å
Forward intensity I(0) i047499300.00
Molecular weight molecular_weight57066.0 kDa
Excluded volume excluded_volume72941 ų
Envelope volume envelope_volume87365 ų
Hydration-shell volume shell_volume27882 ų
Envelope diameter envelope_diameter93.0 Å
Shell Rg shell_rg33.29 Å
Envelope Rg envelope_rg26.45 Å
Shape Rg shape_rg26.47 Å
Total Rg total_rg27.22 Å
Total atoms total_atoms4013
Residues n_residues496
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax86.6 Å
Rg (real space) rg_real27.51 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real4.7500e+07
I(0) uncertainty (real space) i0_real_error6.2970e+05
Rg (reciprocal space) rg_reciprocal27.51 Å
I(0) (reciprocal space) i0_reciprocal47500000.0000
Solution quality estimate total_estimate0.9058
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4 Å
Skewness Skewness skewness0.293
Kurtosis Kurtosis kurtosis-0.607
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12630000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.977
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3d90a_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain
Domain ID domain_idd3d90b_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id3d90A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3d90B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
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8. Citations (1)

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9. Files and Curves (10)