3d57

TR Variant D355R

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: GOOD

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

Thyroid hormone 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 209–460 Chain B； UniProt 209–460	Fragment：C-terminal domain Mutation：D355R	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.240

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 3D57	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BSX STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS Deposited 1998-08-31	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 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	T3 3,5,3'TRIIODOTHYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；pH 4.9	Resolution 3.70 Å R-free 0.299
1BSX STRUCTURE AND SPECIFICITY OF NUCLEAR RECEPTOR-COACTIVATOR INTERACTIONS Deposited 1998-08-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	T3 3,5,3'TRIIODOTHYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；pH 4.9	Resolution 3.70 Å R-free 0.299
1N46 CRYSTAL STRUCTURE OF HUMAN TR BETA LIGAND-BINDING DOMAIN COMPLEXED WITH A POTENT SUBTYPE-SELECTIVE THYROMIMETIC Deposited 2002-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 204–461（258 aa） Chain B 204–461（258 aa）	Not recorded	PFA [4-(4-HYDROXY-3-ISOPROPYL-PHENOXY)-3,5-DIMETHYL-PHENYL]-6-AZAURACIL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0, temperature 100K	Resolution 2.20 Å R-free 0.256
1NAX Thyroid receptor beta1 in complex with a beta-selective ligand Deposited 2002-11-29	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 209–460（252 aa） Fragment：Ligand binding domain (residues 209-460)	Not recorded	IH5 {3,5-DICHLORO-4-[4-HYDROXY-3-(PROPAN-2-YL)PHENOXY]PHENYL}ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulphate, TRIS, NDSB-201, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.237
1NAX Thyroid receptor beta1 in complex with a beta-selective ligand Deposited 2002-11-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 209–460（252 aa） Fragment：Ligand binding domain (residues 209-460)	Not recorded	IH5 {3,5-DICHLORO-4-[4-HYDROXY-3-(PROPAN-2-YL)PHENOXY]PHENYL}ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；ammonium sulphate, TRIS, NDSB-201, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.237
1NQ0 TR Receptor Mutations Conferring Hormone Resistance and Reduced Corepressor Release Exhibit Decreased Stability in the Nterminal LBD Deposited 2003-01-20	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 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：A234T	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 1 ARS ARSENIC × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；700 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.258
1NQ0 TR Receptor Mutations Conferring Hormone Resistance and Reduced Corepressor Release Exhibit Decreased Stability in the Nterminal LBD Deposited 2003-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：A234T	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 2 ARS ARSENIC × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；700 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.258
1NQ1 TR Receptor Mutations Conferring Hormone Resistance and Reduced Corepressor Release Exhibit Decreased Stability in the Nterminal LBD Deposited 2003-01-20	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 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：R243Q	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 1 ARS ARSENIC × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；700 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.287
1NQ1 TR Receptor Mutations Conferring Hormone Resistance and Reduced Corepressor Release Exhibit Decreased Stability in the Nterminal LBD Deposited 2003-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Mutation：R243Q	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 2 ARS ARSENIC × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；700 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.287
1NQ2 Two RTH Mutants with Impaired Hormone Binding Deposited 2003-01-21	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 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	NA SODIUM ION × 1 4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 1 ARS ARSENIC × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；700 mM sodium acetate, 200mM sodium succinate 100mM sodium cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.264
1NQ2 Two RTH Mutants with Impaired Hormone Binding Deposited 2003-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 202–461（260 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	NA SODIUM ION × 2 4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 2 ARS ARSENIC × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；277 K；700 mM sodium acetate, 200mM sodium succinate 100mM sodium cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.264
1NUO Two RTH Mutants with Impaired Hormone Binding Deposited 2003-01-31	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 201–461（261 aa） Fragment：LIGAND BINDING DOMAIN	Not recorded	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；800 mM sodium acetate, 100mM Sodium Cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.302
1Q4X Crystal Structure of Human Thyroid Hormone Receptor beta LBD in complex with specific agonist GC-24 Deposited 2003-08-04	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 209–461（253 aa） Fragment：Ligand Binding Domain	Not recorded	G24 [4-(3-BENZYL-4-HYDROXYBENZYL)-3,5-DIMETHYLPHENOXY]ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；291 K；PEG 3350, sodium acetate, glucose, cymal-2, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.80 Å R-free 0.264
1R6G Crystal structure of the thyroid hormone receptor beta ligand binding domain in complex with a beta selective compound Deposited 2003-10-15	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 203–461（259 aa） Fragment：ligand binding domain	Not recorded	442 2-[3,5-DIBROMO-4-(4-HYDROXY-3-{HYDROXY[(2-PHENYLETHYL)AMINO]METHYL}PHENOXY)PHENYL]ETHANE-1,1-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；Sodium acetate, sodium cacodylate , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.347
1XZX Thyroxine-Thyroid Hormone Receptor Interactions Deposited 2004-11-12	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 X 202–461（260 aa） Fragment：ligand binding domain (residues 202-461)	Not recorded	CAC CACODYLATE ION × 6 T3 3,5,3'TRIIODOTHYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；279 K；sodium acetate, cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.50 Å R-free 0.244
1XZX Thyroxine-Thyroid Hormone Receptor Interactions Deposited 2004-11-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 202–461（260 aa） Fragment：ligand binding domain (residues 202-461)	Not recorded	CAC CACODYLATE ION × 12 T3 3,5,3'TRIIODOTHYRONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；279 K；sodium acetate, cacodylate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.50 Å R-free 0.244
1Y0X Thyroxine-Thyroid Hormone Receptor Interactions Deposited 2004-11-16	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 X 202–461（260 aa） Fragment：ligand binding domain (residues 202-461)	Not recorded	CAC CACODYLATE ION × 6 T44 3,5,3',5'-TETRAIODO-L-THYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；279 K；sodium acetate, cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 3.10 Å R-free 0.266
1Y0X Thyroxine-Thyroid Hormone Receptor Interactions Deposited 2004-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain X 202–461（260 aa） Fragment：ligand binding domain (residues 202-461)	Not recorded	CAC CACODYLATE ION × 12 T44 3,5,3',5'-TETRAIODO-L-THYRONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；279 K；sodium acetate, cacodylate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 3.10 Å R-free 0.266
2J4A Human Thyroid hormone receptor beta ligand binding domain in complex with KB131084 Deposited 2006-08-28	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 209–461（253 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 209-461	Mutation：YES	OEF 3,5-DIBROMO-4-(3-ISOPROPYL-PHENOXY)BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.45 M AMMONIUMSULFATE, 100 MMTRIS PH8.0, 100MM NDSB	Resolution 2.20 Å R-free 0.273
2NLL RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA Deposited 1996-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 104–206（103 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；CRYSTALLIZED FROM 40% PEG 3350 25 MM IMADAZOLE BUFFER, PH 7.0, 400 MM NH4CL, 10 MM DTT, AND 5 MM MGCL2	Resolution 1.90 Å R-free 0.269
2PIN Thyroid receptor beta in complex with inhibitor Deposited 2007-04-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 209–461（253 aa） Fragment：Ligand-binding domain (residues 209-461) Chain B 209–461（253 aa） Fragment：Ligand-binding domain (residues 209-461)	Mutation：D355R Mutation：D355R	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 2 LEG 1-(4-HEXYLPHENYL)PROP-2-EN-1-ONE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.256
3GWS Crystal Structure of T3-Bound Thyroid Hormone Receptor Deposited 2009-04-01	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 X 202–460（259 aa） Fragment：Ligand Binding Domain (UNP residues 202 to 460)	Non-standard monomer：Yes (specific site not provided by mmCIF)	T3 3,5,3'TRIIODOTHYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；100MM SODIUM CACODYLATE, 1.4M SODIUM ACETATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.233
3IMY Structure of TR-beta bound to selective thyromimetic GC-1 Deposited 2009-08-11	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 202–461（260 aa） Fragment：UNP residues 202-461	Non-standard monomer：Yes (specific site not provided by mmCIF)	B72 {4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；100mM NaCac, 1.2M NaAc, 200mM Na succinate, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.55 Å R-free 0.271
3IMY Structure of TR-beta bound to selective thyromimetic GC-1 Deposited 2009-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 202–461（260 aa） Fragment：UNP residues 202-461	Non-standard monomer：Yes (specific site not provided by mmCIF)	B72 {4-[4-hydroxy-3-(1-methylethyl)benzyl]-3,5-dimethylphenoxy}acetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；100mM NaCac, 1.2M NaAc, 200mM Na succinate, pH 7.5, VAPOR DIFFUSION, temperature 291K	Resolution 2.55 Å R-free 0.271
3JZC Crystal Structure of TR-beta bound to the selective thyromimetic TRIAC Deposited 2009-09-23	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 202–461（260 aa） Fragment：UNP residues 202-461, Ligand Binding Domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	4HY [4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；291 K；100mM Sodium Cacodylate, 1.4M sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.246
4ZO1 Crystal Structure of the T3-bound TR-beta Ligand-binding Domain in complex with RXR-alpha Deposited 2015-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain X 210–461（252 aa） Fragment：ligand binding domain unp residues 210-461	Not recorded	T3 3,5,3'TRIIODOTHYRONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；20% PEG 3350, 100 mM Tris pH 8.0, 0.1 M ammonium acetate, and 1 mM Methoprene acid	Resolution 3.22 Å R-free 0.281
6KKB A novel agonist of THRb Deposited 2019-07-24	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 X 211–460（250 aa）	Not recorded	8HO 2-[(1-methyl-4-oxidanyl-7-phenoxy-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium citrate tribasic dihydrate, 20%(w/v) Polyethylene glycol 3,350	Resolution 1.70 Å R-free 0.197
6KKE THRb mutation with a novel agonist Deposited 2019-07-25	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 211–459（249 aa）	Mutation：H435L	8HO 2-[(1-methyl-4-oxidanyl-7-phenoxy-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.2 M Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.58 Å R-free 0.217
6KNU THRb mutation with a novel agonist Deposited 2019-08-07	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 211–460（250 aa）	Mutation：V264D	8HO 2-[(1-methyl-4-oxidanyl-7-phenoxy-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.1M Sodium acetate trihydrate pH 4.6, 2.0M Sodium formate	Resolution 2.70 Å R-free 0.231
6KNV THRb mutation with a novel agonist Deposited 2019-08-07	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 211–460（250 aa）	Mutation：R438W	8HO 2-[(1-methyl-4-oxidanyl-7-phenoxy-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2% v/v Tacsimate pH 5.0, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 16% w/v Polyethylene glycol 3,350	Resolution 2.80 Å R-free 0.265
6KNW THRb mutation with a novel agonist Deposited 2019-08-07	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 211–460（250 aa）	Mutation：R438H	8HO 2-[(1-methyl-4-oxidanyl-7-phenoxy-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100mM Nacl 20% PEG 4000	Resolution 2.67 Å R-free 0.244
7WLX A novel chemical derivative(53) of THRB agonist Deposited 2022-01-14	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 217–476（260 aa）	Not recorded	9GC 2-[[1-methoxy-4-oxidanyl-7-[4-(phenylmethyl)phenoxy]isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2% v/v tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 16% w/v polyethylene glycol 3,350.	Resolution 2.39 Å R-free 0.270
7WMG A novel chemical derivative(52) of THRB agonist Deposited 2022-01-14	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 217–476（260 aa）	Not recorded	9IF 2-[[1-methoxy-4-oxidanyl-7-(4-phenoxyphenoxy)isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium formate pH 7.0 and 20% w/v polyethylene glycol 3,350.	Resolution 2.93 Å R-free 0.298
7WMH A novel chemical derivative(56) of THRB agonist Deposited 2022-01-14	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 217–476（260 aa）	Not recorded	9II 2-[[1-methoxy-4-oxidanyl-7-(4-phenylphenoxy)isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MgSO4 and 5% PEG 8000	Resolution 1.97 Å R-free 0.253
7WMJ A novel chemical derivative(71) of THRB agonist Deposited 2022-01-14	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 217–476（260 aa）	Not recorded	9IL 2-[[7-[2,6-dimethyl-4-(phenylcarbonyl)phenoxy]-1-methoxy-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% v/v ethylene glycol.	Resolution 2.81 Å R-free 0.274
7WML A novel chemical derivative(85) of THRB agonist Deposited 2022-01-15	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 217–476（260 aa）	Not recorded	9IQ 2-[[7-[4-(3,5-dimethylphenyl)carbonyl-2,6-dimethyl-phenoxy]-1-ethoxy-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MgSO4 and 12% PEG 6000.	Resolution 2.67 Å R-free 0.245
7WMN A novel chemical derivative(89) of THRB agonist Deposited 2022-01-15	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 217–476（260 aa）	Not recorded	9IT 2-[[7-[2,6-dimethyl-4-(3-methylphenyl)carbonyl-phenoxy]-1-methoxy-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MgSO4 and 12% PEG 6000.	Resolution 2.57 Å R-free 0.261
7WMO A novel chemical derivative(92) of THRB agonist Deposited 2022-01-15	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 217–476（260 aa）	Not recorded	9IW 2-[[1-ethoxy-7-[4-(3-fluoranyl-5-methoxy-phenyl)carbonyl-2,6-dimethyl-phenoxy]-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium malonate pH 6.0 and 20% w/v Polyethylene glycol 3,350	Resolution 2.56 Å R-free 0.241
8RQN Human thyroid hormone receptor beta ligand binding domain in complex with beta-selective agonist ALG-055009 Deposited 2024-01-18	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 202–461（260 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	A1H2J 6-azanyl-2-[3,5-bis(chloranyl)-4-[(6-oxidanylidene-5-propan-2-yl-1~{H}-pyridazin-3-yl)oxy]phenyl]-1,2,4-triazine-3,5-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.40 M NaAcetate, 0.10 M NaCacodylate pH 7.0	Resolution 2.88 Å R-free 0.262
9IX5 An agonist(compound 15n) of Thyroid Hormone Receptor B Deposited 2024-07-26	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 203–461（259 aa）	Not recorded	A1EAC 2-[(1-methoxy-7-naphthalen-2-yloxy-4-oxidanyl-isoquinolin-3-yl)carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.35 M Sodium citrate tribasic dihydrate, 22%(w/v) Polyethylene glycol 3,350	Resolution 2.65 Å R-free 0.277
9J0K An agonist(compound 14e)of Thyroid Hormone Receptor B Deposited 2024-08-02	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 202–461（260 aa）	Not recorded	A1EAE 2-[[7-[3-(aminomethyl)phenoxy]-1-methoxy-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.3 M ammonium sulfate, 0.1 M MES monohydrate pH 6.7 and 13% v/v 1,4-Dioxane	Resolution 2.70 Å R-free 0.275
9J0K An agonist(compound 14e)of Thyroid Hormone Receptor B Deposited 2024-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 202–461（260 aa）	Not recorded	A1EAE 2-[[7-[3-(aminomethyl)phenoxy]-1-methoxy-4-oxidanyl-isoquinolin-3-yl]carbonylamino]ethanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.3 M ammonium sulfate, 0.1 M MES monohydrate pH 6.7 and 13% v/v 1,4-Dioxane	Resolution 2.70 Å R-free 0.275

33 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	THB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–266； UniProt 209–460 Author chain B； PDBConstruct 15–266； UniProt 209–460

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	3d57
Deposition date deposition_date	2008-05-15
Structure title title	TR Variant D355R
Keywords keywords	;thyroid hormone receptor, ligand binding domain, D355R mutant, homodimer, Alternative splicing, Deafness, Disease mutation, DNA-binding, Metal-binding, Nucleus, Polymorphism, Receptor, Transcription, Transcription regulation, Zinc, Zinc-finger, HORMONE, TRANSCRIPTION RECEPTOR ;; HORMONE, TRANSCRIPTION RECEPTOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.16 Å
Radius of gyration Rg (electron density) rg_electron	25.64 Å
Forward intensity I(0) i0	54150400.00
Molecular weight molecular_weight	57149.0 kDa
Excluded volume excluded_volume	71324 Å³
Envelope volume envelope_volume	86137 Å³
Hydration-shell volume shell_volume	28331 Å³
Envelope diameter envelope_diameter	87.3 Å
Shell Rg shell_rg	32.62 Å
Envelope Rg envelope_rg	25.66 Å
Shape Rg shape_rg	25.63 Å
Total Rg total_rg	26.43 Å
Total atoms total_atoms	3964
Residues n_residues	493
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	84.4 Å
Rg (real space) rg_real	26.16 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	5.4150e+07
I(0) uncertainty (real space) i0_real_error	6.7670e+05
Rg (reciprocal space) rg_reciprocal	26.16 Å
I(0) (reciprocal space) i0_reciprocal	54150000.0000
Solution quality estimate total_estimate	0.8990
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	83.0 Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10950000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.937

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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	Thyroid hormone receptor beta
Molecular weight formula_weight	30127.8 kDa
Mutation mutation	D355R
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	4069

MGSSHHHHHHSQDPGHKPEPTDEEWELIKTVTEAHVATNAQGSHWKQKRKFLPEDIGQAPIVNAPEGGKVDLEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGGLGVVSDAIFRLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFE

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID
Molecular weight formula_weight	621.9 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	105

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d57a_
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	d3d57b_
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	3d57A00
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	3d57B00
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	55.557 Å
Unit-cell length b length_b	92.963 Å
Unit-cell length c length_c	58.808 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.02 °
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	2.200 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2400

fit	/app/data/saxs_computation/d5/3d57/3d57.fit
pddf	/app/data/pr_computation/d5/3d57/3d57.pr.out
profile	/app/data/saxs_computation/d5/3d57/3d57.dat