6l88

Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone

Method: X-RAY DIFFRACTION D_max: 117.0 Å Quality: GOOD

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

Mineralocorticoid receptor

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 735–984 Chain D； UniProt 735–984	Mutation：C808S,C910S	E6R 1-(2-hydroxyethyl)-4-methyl-N-(4-methylsulfonylphenyl)-5-[2-(trifluoromethyl)phenyl]pyrrole-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；2.0-2.5 M sodium nitrate, 0.1 M Tris-HCl pH 8.0	Resolution 3.00 Å R-free 0.307
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 735–984 Chain C； UniProt 735–984	Mutation：C808S,C910S	E6R 1-(2-hydroxyethyl)-4-methyl-N-(4-methylsulfonylphenyl)-5-[2-(trifluoromethyl)phenyl]pyrrole-3-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；2.0-2.5 M sodium nitrate, 0.1 M Tris-HCl pH 8.0	Resolution 3.00 Å R-free 0.307

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 6L88	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y9R Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone and harboring the S810L mutation responsible for a severe form of hypertension Deposited 2004-12-16	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 A 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L, C910A	1CA DESOXYCORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.96 Å R-free 0.267
1Y9R Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone and harboring the S810L mutation responsible for a severe form of hypertension Deposited 2004-12-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L, C910A	1CA DESOXYCORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.96 Å R-free 0.267
1YA3 Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to progesterone and harboring the S810L mutation responsible for a severe form of hypertension Deposited 2004-12-17	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 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L, C910A	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.34 Å R-free 0.284
1YA3 Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to progesterone and harboring the S810L mutation responsible for a severe form of hypertension Deposited 2004-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L, C910A	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.34 Å R-free 0.284
1YA3 Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to progesterone and harboring the S810L mutation responsible for a severe form of hypertension Deposited 2004-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L, C910A	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.34 Å R-free 0.284
2A3I Structural and Biochemical Mechanisms for the Specificity of Hormone Binding and Coactivator Assembly by Mineralocorticoid Receptor Deposited 2005-06-24	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 A 732–984（253 aa） Fragment：Mineralocoricoid receptor	Mutation：C808S	C0R CORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.9；293 K；PEG mme5K, Sodium Acetate, 1-6 Hexanediol, pH 7.9, VAPOR DIFFUSION, temperature 293K	Resolution 1.95 Å R-free 0.253
2AA2 Mineralocorticoid Receptor with Bound Aldosterone Deposited 2005-07-13	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 712–984（273 aa）	Mutation：C808S	BOG octyl beta-D-glucopyranoside × 1 SO4 SULFATE ION × 1 AS4 ALDOSTERONE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH7.5, 0.9M Lithium Sulfate, 2% PEG2KMME, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.235
2AA5 Mineralocorticoid Receptor with Bound Progesterone Deposited 2005-07-13	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 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.264
2AA5 Mineralocorticoid Receptor with Bound Progesterone Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.264
2AA6 Mineralocorticoid Receptor S810L Mutant with Bound Progesterone Deposited 2005-07-13	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 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S, S810L	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 1.95 Å R-free 0.225
2AA6 Mineralocorticoid Receptor S810L Mutant with Bound Progesterone Deposited 2005-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S, S810L	STR PROGESTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 1.95 Å R-free 0.225
2AA7 Mineralocorticoid Receptor with Bound Deoxycorticosterone Deposited 2005-07-13	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 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S	SO4 SULFATE ION × 1 1CA DESOXYCORTICOSTERONE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 2.20 Å R-free 0.264
2AAX Mineralocorticoid Receptor Double Mutant with Bound Cortisone Deposited 2005-07-14	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 712–984（273 aa） Fragment：Ligand Binding Domain Chain B 712–984（273 aa） Fragment：Ligand Binding Domain	Mutation：C808S, S810L Mutation：C808S, S810L	SO4 SULFATE ION × 1 PDN 17,21-DIHYDROXYPREGNA-1,4-DIENE-3,11,20-TRIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 1.75 Å R-free 0.212
2AB2 Mineralocorticoid Receptor Double Mutant with Bound Spironolactone Deposited 2005-07-14	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 712–984（273 aa） Fragment：MR Ligand Binding Domain Chain B 712–984（273 aa） Fragment：MR Ligand Binding Domain	Mutation：C808S, S810L Mutation：C808S, S810L	SNL SPIRONOLACTONE × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1m Hepes pH7.5, 0.9M Li2SO4, 2% PEG 2KMME, vapor diffusion, hanging drop, temperature 298K	Resolution 1.85 Å R-free 0.218
2ABI Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone Deposited 2005-07-15	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 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：C910A	1CA DESOXYCORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；297 K；PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.33 Å R-free 0.264
2ABI Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone Deposited 2005-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：C910A	1CA DESOXYCORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；297 K；PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.33 Å R-free 0.264
2ABI Crystal structure of the human mineralocorticoid receptor ligand-binding domain bound to deoxycorticosterone Deposited 2005-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：C910A	1CA DESOXYCORTICOSTERONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；297 K；PEG4000, HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.33 Å R-free 0.264
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	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 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
2OAX Crystal structure of the S810L mutant mineralocorticoid receptor associated with SC9420 Deposited 2006-12-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 731–984（254 aa） Fragment：LIGAND-BINDING DOMAIN	Mutation：S810L,C910A	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；297 K；HEPES 100 mM, pH 6.8, 230 mM NaCl, 25% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.29 Å R-free 0.263
3VHU Mineralocorticoid receptor ligand-binding domain with spironolactone Deposited 2011-09-07	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 712–984（273 aa） Fragment：LIGAND-BINDING DOMAIN, UNP residues 712-984	Mutation：C808S, S810L	SNL SPIRONOLACTONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M HEPES pH 7.0, 1.26M Lithium sulfate, 6% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.11 Å R-free 0.246
3VHV Mineralocorticoid receptor ligand-binding domain with non-steroidal antagonist Deposited 2011-09-07	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 727–984（258 aa） Fragment：LIGAND-BINDING DOMAIN, UNP residues 727-984	Mutation：C808S, S810L, A976V	LD1 6-[(7S)-7-phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl]-2H-1,4-benzoxazin-3(4H)-one × 1 LD2 6-[(1E)-2-phenyl-N-(3-sulfanyl-4H-1,2,4-triazol-4-yl)ethanimidoyl]-2H-1,4-benzoxazin-3(4H)-one × 1 EDO 1,2-ETHANEDIOL × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；0.1M HEPES pH 7.4, 0.88M potassium/sodium tartrate, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.35 Å R-free 0.167
3WFF Mineralocorticoid receptor ligand-binding domain with compound 2b Deposited 2013-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 712–984（273 aa） Fragment：LIGAND-BINDING DOMAIN, UNP residues 712-984	Mutation：C808S, S810L, A976V	WFF 6-[4-(2,4-difluorophenyl)-5-oxo-2,5-dihydrofuran-3-yl]-2H-1,4-benzoxazin-3(4H)-one × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；0.04M potassium dihydrogen phosphate, 16% PEG 8000, 20% glycerol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.05 Å R-free 0.216
3WFG Mineralocorticoid receptor ligand-binding domain with compuond 2e Deposited 2013-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 712–984（273 aa） Fragment：LIGAND-BINDING DOMAIN, UNP residues 712-984	Mutation：C808S, S810L, A976V	WFG 6-[(2S)-4-(4-fluorophenyl)-2-methyl-5-oxo-2,5-dihydrofuran-3-yl]-2H-1,4-benzoxazin-3(4H)-one × 1 EDO 1,2-ETHANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；0.1M Tris, 23% ethanol, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.40 Å R-free 0.179
4PF3 Mineralocorticoid receptor ligand-binding domain with compuond 37a Deposited 2014-04-28	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 716–988（273 aa） Fragment：UNP residues 716-988	Mutation：C808S, S810L, A976V	HFN 6-[1-(2,2-difluoro-3-hydroxypropyl)-5-(4-fluorophenyl)-3-methyl-1H-pyrazol-4-yl]-2H-1,4-benzoxazin-3(4H)-one × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris pH 8.0, 23% ethanol	Resolution 1.10 Å R-free 0.177
4TNT Structure of the human mineralocorticoid receptor in complex with DNA Deposited 2014-06-04	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 593–671（79 aa） Chain B 593–671（79 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M sodium malonate, 12 % PEG 3350	Resolution 2.39 Å R-free 0.258
4UDA MR in complex with dexamethasone Deposited 2014-12-09	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 735–984（250 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 735-984	Mutation：YES	GOL GLYCEROL × 1 DEX DEXAMETHASONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；30% PEG4000, 0.1M NACL, 0.2M PIPES PH 7.5	Resolution 2.03 Å R-free 0.240
4UDB MR in complex with desisobutyrylciclesonide Deposited 2014-12-09	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 735–984（250 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 735-984	Mutation：YES	DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 CV7 DESISOBUYTYRYL CICLESONIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；18% PEG4K, 0.14M LISO4, 85MM TRIS PH 8.5, 15% GLYCEROL	Resolution 2.36 Å R-free 0.218
5HCV Identification of Spirooxindole and Dibenzoxazepine Motifs as Potent Mineralocorticoid Receptor Antagonists Deposited 2016-01-04	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 732–984（253 aa） Fragment：ligand-binding domain (UNP residues 732-984)	Mutation：C808S	60R 6-[(~{E})-(3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene)methyl]-4~{H}-1,4-benzoxazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；1uL of protein complex at 8-10mg protein/ml is mixed with an equal volume of reservoir solution composed of 100mM Tris-HCl pH=8.0, 200mM NaCl, 5% (v/v) glycerol, 16%(w/v) PEG3350	Resolution 2.50 Å R-free 0.256
5HCV Identification of Spirooxindole and Dibenzoxazepine Motifs as Potent Mineralocorticoid Receptor Antagonists Deposited 2016-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 732–984（253 aa） Fragment：ligand-binding domain (UNP residues 732-984)	Mutation：C808S	60R 6-[(~{E})-(3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene)methyl]-4~{H}-1,4-benzoxazin-3-one × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；1uL of protein complex at 8-10mg protein/ml is mixed with an equal volume of reservoir solution composed of 100mM Tris-HCl pH=8.0, 200mM NaCl, 5% (v/v) glycerol, 16%(w/v) PEG3350	Resolution 2.50 Å R-free 0.256
5HCV Identification of Spirooxindole and Dibenzoxazepine Motifs as Potent Mineralocorticoid Receptor Antagonists Deposited 2016-01-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 732–984（253 aa） Fragment：ligand-binding domain (UNP residues 732-984)	Mutation：C808S	60R 6-[(~{E})-(3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene)methyl]-4~{H}-1,4-benzoxazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；1uL of protein complex at 8-10mg protein/ml is mixed with an equal volume of reservoir solution composed of 100mM Tris-HCl pH=8.0, 200mM NaCl, 5% (v/v) glycerol, 16%(w/v) PEG3350	Resolution 2.50 Å R-free 0.256
5L7E MCR IN COMPLEX WITH ligand Deposited 2016-06-03	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 735–984（250 aa）	Not recorded	NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 6Q0 ~{N}-[[4-(3,5-dimethyl-1,2-oxazol-4-yl)phenyl]methyl]benzenesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；1.6 M AMS 0.1 M CHES pH 9.5 15% EG 10% Morpheus F12	Resolution 1.86 Å R-free 0.197
5L7G MCR IN COMPLEX WITH ligand Deposited 2016-06-03	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 739–988（250 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 6QE ~{N}-[[4-[5-[[2,3-bis(fluoranyl)phenoxy]methyl]-3-methyl-1,2-oxazol-4-yl]phenyl]methyl]-1-methyl-cyclopropane-1-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.9 M AMS 0.1 M CHES pH 9.5 +10% Morpheus C9	Resolution 2.01 Å R-free 0.243
5L7H MCR IN COMPLEX WITH ligand Deposited 2016-06-03	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 735–984（250 aa）	Not recorded	6QG 3-methyl-5,8-dioxa-17lambda-thia-4,18-diazatetracyclo[18.2.2.1,.0]pentacosa-1(22),2(6),3,9,11,13(25),20,23-octaene-17,17-dione × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.9 M AMS 0.1 M CHES pH 9.5 +10% Morpheus G5	Resolution 1.84 Å R-free 0.224
5MWP The structure of MR in complex with AZD9977. Deposited 2017-01-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 735–984（250 aa）	Mutation：C808S, C910S	ECV 2-[(3~{S})-7-fluoranyl-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]-~{N}-methyl-ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M (NH4)2SO4, 0.1 M CHES pH 9.5, and 10% (v/v) of conditions E5 from the Morpheus Screen (Molecular Dimensions).	Resolution 1.82 Å R-free 0.242
5MWY The structure of MR in complex with eplerenone. Deposited 2017-01-20	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 735–984（250 aa）	Not recorded	YNU eplerenone × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M (NH4)2SO4, 0.1 M CHES pH 9.5, and 10% (v/v) of conditions G6 from the Morpheus Screen (Molecular Dimensions)	Resolution 1.75 Å R-free 0.245
6GEV Mineralocorticoid receptor in complex with (s)-13 Deposited 2018-04-27	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 735–984（250 aa）	Not recorded	GOL GLYCEROL × 3 EWN 6-[[(3~{S})-7-fluoranyl-3-(2-methylpropyl)-2,3-dihydro-1,4-benzoxazin-4-yl]carbonyl]-4~{H}-1,4-benzoxazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M (NH4)2SO4, 3.5% 1,4-butanediol, 0.1 M CHES pH 9.5	Resolution 1.54 Å R-free 0.190
6GG8 Mineralocorticoid receptor in complex with (s)-13 Deposited 2018-05-03	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 735–984（250 aa）	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 EY8 [(3~{R})-7-fluoranyl-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]methanesulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9M (NH4)2SO4, 0.1 M CHES pH9.5, 10% (v/v) of condition C8 of the Morpheus Screen (Molecular Dimension)	Resolution 1.80 Å R-free 0.228
6GGG Mineralocorticoid receptor in complex with (s)-13 Deposited 2018-05-03	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 735–984（250 aa）	Not recorded	CL CHLORIDE ION × 1 EYN 2-[(3~{S})-7-fluoranyl-6-(2-methylpropyl)-4-[(3-oxidanylidene-4~{H}-1,4-benzoxazin-6-yl)carbonyl]-2,3-dihydro-1,4-benzoxazin-3-yl]-~{N}-methyl-ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Condition C2 of the morpheus screen (Molecular Dimension).	Resolution 1.71 Å R-free 0.192
9GC7 Mineralocorticoid receptor in complex with acylurea antagonists. Deposited 2024-08-01	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 A 735–984（250 aa）	Mutation：C808S, S810L, C910S	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 A1IJ6 (2S)-N-aminocarbonyl-2-[(4-cyano-6-cyclopropyl-cyclohexa-1,2,3,5-tetraen-1-yl)amino]propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.9 M AMS 0.1 M CHES pH 9.5 +10% Morpheus G8	Resolution 1.46 Å R-free 0.210

29 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MCR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–251； UniProt 735–984 Author chain B； PDBConstruct 2–251； UniProt 735–984 Author chain C； PDBConstruct 2–251； UniProt 735–984 Author chain D； PDBConstruct 2–251； UniProt 735–984

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	6l88
Deposition date deposition_date	2019-11-05
Structure title title	Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone
Keywords keywords	Nuclear receptor, Hypertension, NUCLEAR PROTEIN, 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	36.80 Å
Radius of gyration Rg (electron density) rg_electron	36.08 Å
Forward intensity I(0) i0	109989000.00
Molecular weight molecular_weight	88400.0 kDa
Excluded volume excluded_volume	112460 Å³
Envelope volume envelope_volume	153230 Å³
Hydration-shell volume shell_volume	36606 Å³
Envelope diameter envelope_diameter	120.1 Å
Shell Rg shell_rg	40.89 Å
Envelope Rg envelope_rg	35.56 Å
Shape Rg shape_rg	36.09 Å
Total Rg total_rg	36.43 Å
Total atoms total_atoms	6212
Residues n_residues	755
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	117.0 Å
Rg (real space) rg_real	36.81 Å
Rg uncertainty (real space) rg_real_error	1.53 Å
I(0) (real space) i0_real	1.1000e+08
I(0) uncertainty (real space) i0_real_error	1.9820e+06
Rg (reciprocal space) rg_reciprocal	36.81 Å
I(0) (reciprocal space) i0_reciprocal	110000000.0000
Solution quality estimate total_estimate	0.8807
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.7 Å
Skewness Skewness skewness	0.189
Kurtosis Kurtosis kurtosis	-0.711
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29480000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.791

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6l88a_
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	d6l88b_
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	d6l88c_
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	d6l88d_
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

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8. Citations (1)

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Unit-cell length a length_a	160.888 Å
Unit-cell length b length_b	160.888 Å
Unit-cell length c length_c	160.888 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	48

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2705
R_work r_work	0.2685
R_free r_free	0.3070

Description description	Mineralocorticoid receptor
Molecular weight formula_weight	29159.7 kDa
Mutation mutation	C808S,C910S
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6218

Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone

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

Mineralocorticoid receptor

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	1-(2-hydroxyethyl)-4-methyl-N-(4-methylsulfonylphenyl)-5-[2-(trifluoromethyl)phenyl]pyrrole-3-carboxamide
Molecular weight formula_weight	466.5 kDa
Source method src_method	syn
Copy count entity_count	4

fit	/app/data/saxs_computation/l8/6l88/6l88.fit
pddf	/app/data/pr_computation/l8/6l88/6l88.pr.out
profile	/app/data/saxs_computation/l8/6l88/6l88.dat