1u9e

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397

Method: X-RAY DIFFRACTION D_max: 70.2 Å Quality: EXCELLENT

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

Estrogen receptor beta

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 261–501	Not recorded	STEROID RECEPTOR COACTIVATOR-1 × 1 397 2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG3350, Mg formate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.279
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 261–501	Not recorded	STEROID RECEPTOR COACTIVATOR-1 × 1 397 2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG3350, Mg formate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.279
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 261–501 Chain B； UniProt 261–501	Not recorded	STEROID RECEPTOR COACTIVATOR-1 × 2 397 2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；PEG3350, Mg formate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 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 1U9E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L2J Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol Deposited 2002-02-21	Different construct 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 256–505（250 aa） Fragment：ligand-binding domain (residues 256-505)	Not recorded	ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；1.5-1.75 M Ammonium sulfate, 100 mM Sodium Acetate pH 4.8-5.2 294-296 K, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.95 Å R-free 0.299
1L2J Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol Deposited 2002-02-21	Different construct 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 256–505（250 aa） Fragment：ligand-binding domain (residues 256-505)	Not recorded	ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；1.5-1.75 M Ammonium sulfate, 100 mM Sodium Acetate pH 4.8-5.2 294-296 K, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.95 Å R-free 0.299
1L2J Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol Deposited 2002-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 256–505（250 aa） Fragment：ligand-binding domain (residues 256-505)	Not recorded	ETC (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；295 K；1.5-1.75 M Ammonium sulfate, 100 mM Sodium Acetate pH 4.8-5.2 294-296 K, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.95 Å R-free 0.299
1NDE Estrogen Receptor beta with Selective Triazine Modulator Deposited 2002-12-09	Different construct 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 256–501（246 aa） Fragment：residues 256-501	Not recorded	MON 4-(2-{[4-{[3-(4-CHLOROPHENYL)PROPYL]SULFANYL}-6-(1-PIPERAZINYL)-1,3,5-TRIAZIN-2-YL]AMINO}ETHYL)PHENOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；50mM PIPES pH6.5, 200 mM lithium sulfate, 8-12% PEG35000, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K	Resolution 3.00 Å R-free 0.273
1NDE Estrogen Receptor beta with Selective Triazine Modulator Deposited 2002-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–501（246 aa） Fragment：residues 256-501	Not recorded	MON 4-(2-{[4-{[3-(4-CHLOROPHENYL)PROPYL]SULFANYL}-6-(1-PIPERAZINYL)-1,3,5-TRIAZIN-2-YL]AMINO}ETHYL)PHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；50mM PIPES pH6.5, 200 mM lithium sulfate, 8-12% PEG35000, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K	Resolution 3.00 Å R-free 0.273
1NDE Estrogen Receptor beta with Selective Triazine Modulator Deposited 2002-12-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 256–501（246 aa） Fragment：residues 256-501	Not recorded	MON 4-(2-{[4-{[3-(4-CHLOROPHENYL)PROPYL]SULFANYL}-6-(1-PIPERAZINYL)-1,3,5-TRIAZIN-2-YL]AMINO}ETHYL)PHENOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；50mM PIPES pH6.5, 200 mM lithium sulfate, 8-12% PEG35000, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K	Resolution 3.00 Å R-free 0.273
1QKM HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN Deposited 1999-07-27	Different construct 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 255–509（255 aa） Fragment：LIGAND-BINDING DOMAIN	Not recorded	GEN GENISTEIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；6-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1	Resolution 1.80 Å R-free 0.252
1U3Q Crystal Structure of Estrogen Receptor beta complexed with CL-272 Deposited 2004-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Chain C 261–500（240 aa）	Not recorded	272 4-(6-HYDROXY-BENZO[D]ISOXAZOL-3-YL)BENZENE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG2000, MgCl, hexaminecobalt trichloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.279
1U3Q Crystal Structure of Estrogen Receptor beta complexed with CL-272 Deposited 2004-07-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Chain D 261–500（240 aa）	Not recorded	272 4-(6-HYDROXY-BENZO[D]ISOXAZOL-3-YL)BENZENE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG2000, MgCl, hexaminecobalt trichloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.279
1U3R Crystal Structure of Estrogen Receptor beta complexed with WAY-338 Deposited 2004-07-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–501（241 aa） Chain B 261–501（241 aa）	Not recorded	338 2-(5-HYDROXY-NAPHTHALEN-1-YL)-1,3-BENZOOXAZOL-6-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；PEG3350, Mg formate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.21 Å R-free 0.267
1U3S Crystal Structure of Estrogen Receptor beta complexed with WAY-797 Deposited 2004-07-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	797 3-(6-HYDROXY-NAPHTHALEN-2-YL)-BENZO[D]ISOOXAZOL-6-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；PEG3350, Mg formate , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.250
1X76 CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-697 Deposited 2004-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	697 5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-CARBONITRILE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；PEG3350, Mg Formate, pH 5.90, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.265
1X78 CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-244 Deposited 2004-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	244 [5-HYDROXY-2-(4-HYDROXYPHENYL)-1-BENZOFURAN-7-YL]ACETONITRILE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；291 K；PEG3350, Mg Formate, pH 5.90, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.270
1X7B CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH ERB-041 Deposited 2004-08-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	041 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG3350, Mg Formate, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.266
1X7J CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH GENISTEIN Deposited 2004-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	GEN GENISTEIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG2000, MgCL., pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.282
1ZAF Crystal structure of estrogen receptor beta complexed with 3-Bromo-6-hydroxy-2-(4-hydroxy-phenyl)-inden-1-one Deposited 2005-04-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 263–500（238 aa） Chain B 263–500（238 aa）	Not recorded	789 3-BROMO-6-HYDROXY-2-(4-HYDROXYPHENYL)-1H-INDEN-1-ONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；15% PEG3350, 0.2M Mg Acetate, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.20 Å R-free 0.286
2FSZ A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta Deposited 2006-01-23	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 257–502（246 aa） Fragment：ligand-binding domain Chain B 257–502（246 aa） Fragment：ligand-binding domain	Mutation：C334S, C369S, C481S Mutation：C334S, C369S, C481S	OHT 4-HYDROXYTAMOXIFEN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；0.1M sodium citrate, 1.5M sodium chloride, 4% ethylene imine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.299
2FSZ A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta Deposited 2006-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 257–502（246 aa） Fragment：ligand-binding domain Chain B 257–502（246 aa） Fragment：ligand-binding domain	Mutation：C334S, C369S, C481S Mutation：C334S, C369S, C481S	OHT 4-HYDROXYTAMOXIFEN × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；0.1M sodium citrate, 1.5M sodium chloride, 4% ethylene imine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.20 Å R-free 0.299
2GIU Human estrogen receptor beta ligand-binding domain in complex with compound 45 Deposited 2006-03-29	Different construct 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 260–500（241 aa） Fragment：LIGAND-BINDING DOMAIN (Residues 260-500)	Not recorded	FBR (9aS)-4-bromo-9a-butyl-7-hydroxy-1,2,9,9a-tetrahydro-3H-fluoren-3-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Precipitant 1.8 M NaCl, 6% PEG 6000, 3% isopropanol, 50 mM Tris buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.20 Å R-free 0.323
2I0G Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia Deposited 2006-08-10	Different construct 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 256–505（250 aa） Chain B 256–505（250 aa）	Not recorded	I0G (3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；289 K；0.1M Tris, pH 8.0, 2M sodium chloride, 4% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.50 Å R-free 0.271
2JJ3 Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist Deposited 2007-07-03	Different construct 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 256–505（250 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 256-505 Chain B 256–505（250 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 256-505	Not recorded	JJ3 (3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-6-(METHOXYMETHYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；2M NACL, 9% PEG 6,000, 100MM TRIS PH 8.0	Resolution 2.28 Å R-free 0.255
2NV7 Crystal Structure of Estrogen Receptor Beta Complexed with WAY-555 Deposited 2006-11-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 263–500（238 aa） Chain B 263–500（238 aa）	Not recorded	555 4-(4-HYDROXYPHENYL)-1-NAPHTHALDEHYDE OXIME × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；precipitant: PEG3350, Mg formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.10 Å R-free 0.265
2QTU Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand Deposited 2007-08-02	Different construct 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 256–505（250 aa） Fragment：ligand binding domain Chain B 256–505（250 aa） Fragment：ligand binding domain	Not recorded	3AS (3aS,4R,9bR)-2,2-difluoro-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；0.1 M Tris-HCl, 2 M NaCl, 4% PEG 6000, pH 8.0, VAPOR DIFFUSION, temperature 289K	Resolution 2.53 Å R-free 0.279
2YJD Stapled peptide bound to Estrogen Receptor Beta Deposited 2011-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 261-500 Chain B 261–500（240 aa） Fragment：LIGAND-BINDING DOMAIN, RESIDUES 261-500	Not recorded	YJD 4-(2-PROPAN-2-YLOXYBENZIMIDAZOL-1-YL)PHENOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.93 Å R-free 0.260
2YLY Sulfonamides as selective Estrogen Receptor beta Agonists. Deposited 2011-06-06	Different construct 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 260–500（241 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 260-500 Chain B 260–500（241 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 260-500	Not recorded	SU4 N-cyclopropyl-4-oxidanyl-N-[(2R)-2-oxidanyl-2-phenyl-propyl]benzenesulfonamide × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.275
2Z4B Estrogen receptor beta ligand-binding domain complexed to a benzopyran ligand Deposited 2007-06-14	Different construct 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 256–505（250 aa） Fragment：ligand-binding domain (Residues 251-505) Chain B 256–505（250 aa） Fragment：ligand-binding domain (Residues 251-505)	Not recorded	DC8 (3AS,4R,9BR)-2,2-DIFLUORO-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；289 K；0.1M Tris, pH 8.0, 2M sodium chloride, 4% PEG 6000, VAPOR DIFFUSION, temperature 289.0K	Resolution 2.34 Å R-free 0.253
3OLL Crystal structure of phosphorylated estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Non-standard monomer：Yes (specific site not provided by mmCIF)	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.50 Å R-free 0.208
3OLL Crystal structure of phosphorylated estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Non-standard monomer：Yes (specific site not provided by mmCIF)	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.50 Å R-free 0.208
3OLL Crystal structure of phosphorylated estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500) Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.50 Å R-free 0.208
3OLS Crystal structure of estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.20 Å R-free 0.266
3OLS Crystal structure of estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.20 Å R-free 0.266
3OLS Crystal structure of estrogen receptor beta ligand binding domain Deposited 2010-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500) Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.20 Å R-free 0.266
3OMO Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	WV7 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-6-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.21 Å R-free 0.264
3OMO Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	WV7 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-6-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.21 Å R-free 0.264
3OMO Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500) Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	WV7 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-6-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.21 Å R-free 0.264
3OMP Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W14 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-7-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.05 Å R-free 0.255
3OMP Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W14 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-7-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.05 Å R-free 0.255
3OMP Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500) Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W14 2-(trifluoroacetyl)-1,2,3,4-tetrahydroisoquinolin-7-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.05 Å R-free 0.255
3OMQ Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W23 2-[(trifluoromethyl)sulfonyl]-1,2,3,4-tetrahydroisoquinolin-6-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.97 Å R-free 0.260
3OMQ Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W23 2-[(trifluoromethyl)sulfonyl]-1,2,3,4-tetrahydroisoquinolin-6-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.97 Å R-free 0.260
3OMQ Fragment-Based Design of novel Estrogen Receptor Ligands Deposited 2010-08-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500) Chain B 261–500（240 aa） Fragment：Ligand Binding Domain (UNP residues 261-500)	Not recorded	W23 2-[(trifluoromethyl)sulfonyl]-1,2,3,4-tetrahydroisoquinolin-6-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277.15 K；0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 5.5, 17% PEG10000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 1.97 Å R-free 0.260
4J24 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：;Ligand Binding Domain, UNP residue 261-500' ;	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；0.2M Magnesium acetate, 20%(w/v) PEG3350, pH 4.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.224
4J24 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：;Ligand Binding Domain, UNP residue 261-500' ;	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；0.2M Magnesium acetate, 20%(w/v) PEG3350, pH 4.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.224
4J24 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 261–500（240 aa） Fragment：;Ligand Binding Domain, UNP residue 261-500' ;	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；0.2M Magnesium acetate, 20%(w/v) PEG3350, pH 4.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.224
4J24 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 261–500（240 aa） Fragment：;Ligand Binding Domain, UNP residue 261-500' ;	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；0.2M Magnesium acetate, 20%(w/v) PEG3350, pH 4.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.10 Å R-free 0.224
4J26 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 261–500（240 aa） Fragment：Ligand Binding Domain, UNP residues 261-500	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；10%-20% PEG6000, 0.6M-2M LiCl, 100mM Citric Acid, pH 5.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.242
4J26 Estrogen Receptor in complex with proline-flanked LXXLL peptides Deposited 2013-02-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 261–500（240 aa） Fragment：Ligand Binding Domain, UNP residues 261-500	Not recorded	EST ESTRADIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；277 K；10%-20% PEG6000, 0.6M-2M LiCl, 100mM Citric Acid, pH 5.0, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.242
4ZI1 HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE Deposited 2015-04-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 262–509（248 aa） Fragment：LIGAND BINDING DOMAIN, UNP residues 262-509	Not recorded	KB0 2-(4-hydroxyphenyl)-7-methyl-3-phenyl-1H-inden-5-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.2；293 K；10.5% (W/V) P6000, 1.75M NACL 0.1 M MES, PH 5.2, 12.5% (V/V) GLYCEROL, 2 TIMES EXCESS OF CIA12 PEPTIDE	Resolution 2.10 Å R-free 0.223
5TOA Crystal Structure of ER beta bound to Estradiol Deposited 2016-10-17	Different construct 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 262–509（248 aa） Fragment：UNP residues 262-509 Chain B 262–509（248 aa） Fragment：UNP residues 262-509	Not recorded	EST ESTRADIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；0.1 M Na-citrate, 10% [w/v] PEG-4000, 10% [v/v] isopropanol	Resolution 2.50 Å R-free 0.244
7XVY Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN Deposited 2022-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：ligand-binding domain Chain B 261–500（240 aa） Fragment：ligand-binding domain	Mutation：C334S, C369S, C481S Mutation：C334S, C369S, C481S	I0K (2~{S})-2,3-bis(4-hydroxyphenyl)propanenitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate	Resolution 1.54 Å R-free 0.237
7XVZ Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile Deposited 2022-05-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：ligand-binding domain Chain B 261–500（240 aa） Fragment：ligand-binding domain	Mutation：C334S,C369S,C481S Mutation：C334S,C369S,C481S	I1D (2~{R})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate	Resolution 2.08 Å R-free 0.307
7XWP Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile Deposited 2022-05-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：ligand-binding domain Chain B 261–500（240 aa） Fragment：ligand-binding domain	Mutation：C334S,C369S,C481S Mutation：C334S,C369S,C481S	I1I (2~{S})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate	Resolution 1.92 Å R-free 0.255
7XWQ Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile Deposited 2022-05-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：ligand-binding domain Chain B 261–500（240 aa） Fragment：ligand-binding domain	Mutation：C334S,C369S,C481S Mutation：C334S,C369S,C481S	I1M (2~{R})-2-(2-chloranyl-4-oxidanyl-phenyl)-3-(4-hydroxyphenyl)propanenitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate	Resolution 1.89 Å R-free 0.239
7XWR Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile Deposited 2022-05-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Fragment：ligand-binding domain Chain B 261–500（240 aa） Fragment：ligand-binding domain	Mutation：C334S,C369S,C481S Mutation：C334S,C369S,C481S	I2B (2~{S})-2-(2-chloranyl-4-oxidanyl-phenyl)-3-(4-hydroxyphenyl)propanenitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate	Resolution 2.16 Å R-free 0.318
9EBL Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 1) Deposited 2024-11-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: octameric	Chain A 262–500（239 aa） Chain B 262–500（239 aa） Chain E 262–500（239 aa） Chain F 262–500（239 aa）	Not recorded	B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1 M sodium HEPES pH 7.5, 22% w/v PEG 5000 MME	Resolution 2.20 Å R-free 0.277
9ECF Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2) Deposited 2024-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 261–500（240 aa） Chain F 261–500（240 aa）	Not recorded	B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350	Resolution 2.00 Å R-free 0.278
9ECF Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2) Deposited 2024-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 261–500（240 aa） Chain B 261–500（240 aa）	Not recorded	B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350	Resolution 2.00 Å R-free 0.278
9ECF Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2) Deposited 2024-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 261–500（240 aa） Chain J 261–500（240 aa）	Not recorded	B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350	Resolution 2.00 Å R-free 0.278
9ECF Crystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2) Deposited 2024-11-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 261–500（240 aa） Chain N 261–500（240 aa）	Not recorded	B81 (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350	Resolution 2.00 Å R-free 0.278

36 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ESR2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 261–501 Author chain B； PDBConstruct 1–241； UniProt 261–501

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	1u9e
Deposition date deposition_date	2004-08-09
Structure title title	CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397
Keywords keywords	ESTROGEN RECEPTOR, ESTROGEN RECEPTOR BETA, ER-BETA, ER, ESTROGEN, NUCLEAR RECEPTOR, TRANSCRIPTION FACTOR, AGONIST, TRANSCRIPTION; TRANSCRIPTION
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	23.22 Å
Radius of gyration Rg (electron density) rg_electron	22.25 Å
Forward intensity I(0) i0	43105300.00
Molecular weight molecular_weight	53576.0 kDa
Excluded volume excluded_volume	68351 Å³
Envelope volume envelope_volume	79234 Å³
Hydration-shell volume shell_volume	28678 Å³
Envelope diameter envelope_diameter	73.1 Å
Shell Rg shell_rg	29.90 Å
Envelope Rg envelope_rg	22.31 Å
Shape Rg shape_rg	22.27 Å
Total Rg total_rg	23.09 Å
Total atoms total_atoms	3741
Residues n_residues	469
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	70.2 Å
Rg (real space) rg_real	23.05 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	4.3110e+07
I(0) uncertainty (real space) i0_real_error	5.0140e+05
Rg (reciprocal space) rg_reciprocal	23.09 Å
I(0) (reciprocal space) i0_reciprocal	43110000.0000
Solution quality estimate total_estimate	0.9067
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.2 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16470000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.999

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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	Estrogen receptor beta
Molecular weight formula_weight	27266.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3848

DALSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLR

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(DE3)

Entity 2 Entity 2 polymer

Description description	STEROID RECEPTOR COACTIVATOR-1
Molecular weight formula_weight	1017.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

KLVQLLTTT

Entity 3 Entity 3 non-polymer

Description description	2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL
Molecular weight formula_weight	226.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1u9ea_
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	d1u9eb_
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	1u9eA00
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	1u9eB00
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	52.113 Å
Unit-cell length b length_b	87.935 Å
Unit-cell length c length_c	99.524 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	19.850 Å
R factor r_factor	0.2340
R_work r_work	0.2310
R_free r_free	0.2790

fit	/app/data/saxs_computation/u9/1u9e/1u9e.fit
pddf	/app/data/pr_computation/u9/1u9e/1u9e.pr.out
profile	/app/data/saxs_computation/u9/1u9e/1u9e.dat

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397

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

Estrogen receptor beta

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)