5nky

Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain

Method: X-RAY DIFFRACTION D_max: 61.8 Å Quality: GOOD

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

Vitamin D3 receptor A

Danio rerio

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 156–453	Not recorded	SRC1 × 2 91W (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；0.1 M BTP pH 7.0, 3 M NaOAc	Resolution 2.10 Å R-free 0.246

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 5NKY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2HBH Crystal structure of Vitamin D nuclear receptor ligand binding domain bound to a locked side-chain analog of calcitriol and SRC-1 peptide Deposited 2006-06-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain	Not recorded	XE4 1,3-CYCLOHEXANEDIOL, 4-METHYLENE-5-[(2E)-[(1S,3AS,7AS)-OCTAHYDRO-1-(5-HYDROXY-5-METHYL-1,3-HEXADIYNYL)-7A-METHYL-4H-INDEN-4-YLIDENE]ETHYLIDENE]-, (1R,3S,5Z) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Li sulfate 1.6M, Mg sulfate 50mM, Bis Tris 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.65 Å R-free 0.261
2HC4 Crystal structure of the LBD of VDR of Danio rerio in complex with calcitriol Deposited 2006-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Li sulfate 1.6M, Mg sulfate 50mM, Bis Tris 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.250
2HCD Crystal structure of the ligand binding domain of the Vitamin D nuclear receptor in complex with Gemini and a coactivator peptide Deposited 2006-06-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain	Not recorded	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Li sulfate 1.6M, Mgsulfate 50mM, Bis tris 0.1M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.260
3DR1 Side-chain fluorine atoms of non-steroidal vitamin D3 analogs stabilize helix 12 of vitamin D receptor Deposited 2008-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain	Not recorded	MG MAGNESIUM ION × 2 C5D (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Li sulfate 1.6M, Mg sulfate 50mM, Bis Tris 0.1M , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.286
3O1D Structure-function study of Gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097. Deposited 2010-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand Binding Domain (UNP Residues 156-453)	Not recorded	G72 (1R,3R,7E,17beta)-17-[(1S)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,10-secoestra-5,7-diene-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；50 mM BIS-TRIS pH6.5, 1.6 M lithium sulfate, 50 mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.40 Å R-free 0.267
3O1E Structure-function of Gemini derivatives with two different side chains at C-20, Gemini-0072 and Gemini-0097. Deposited 2010-07-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand Binding Domain (UNP Residues 156-453)	Not recorded	H97 (1R,3R,7E,17beta)-17-[(1R)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,1 0-secoestra-5,7-diene-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；50 mM BIS-TRIS pH6.5, 1.6 M lithium sulfate, 50 mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.50 Å R-free 0.272
4FHH Development of synthetically accessible non-secosteroidal hybrid molecules combining vitamin D receptor agonism and histone deacetylase inhibition Deposited 2012-06-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：UNP RESIDUES 156-453	Not recorded	0U3 N-hydroxy-2-{4-[3-(4-{[(2S)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}acetamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；Bis Tris 0.1M, lithium sulfate 1.6M and magnesium sulfate 50 mM, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5	Resolution 2.33 Å R-free 0.258
4G1D Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	0VK 3-(5'-{[3,4-bis(hydroxymethyl)benzyl]oxy}-2'-methyl-2-propylbiphenyl-4-yl)pentan-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.5	Resolution 2.90 Å R-free 0.291
4G1Y Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	0VO (4E,6Z)-7-(3-{[3,4-bis(hydroxymethyl)benzyl]oxy}phenyl)-3-ethylnona-4,6-dien-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.85 Å R-free 0.270
4G1Z Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	0VP 3-(5'-{[3,4-bis(hydroxymethyl)benzyl]oxy}-2'-ethyl-2-propylbiphenyl-4-yl)pentan-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.5	Resolution 2.50 Å R-free 0.274
4G20 Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	484 3-(5'-{2-[3,4-bis(hydroxymethyl)phenyl]ethyl}-2'-methyl-2-propylbiphenyl-4-yl)pentan-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.287
4G21 Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	0VP 3-(5'-{[3,4-bis(hydroxymethyl)benzyl]oxy}-2'-ethyl-2-propylbiphenyl-4-yl)pentan-3-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.90 Å R-free 0.291
4G2H Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：unp residues 156-453	Not recorded	0VQ (3E,5E)-6-(3-{2-[3,4-bis(hydroxymethyl)phenyl]ethyl}phenyl)-1,1,1-trifluoro-2-(trifluoromethyl)octa-3,5-dien-2-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5	Resolution 2.50 Å R-free 0.285
4IA1 Diastereotopic and Deuterium Effects in Gemini Deposited 2012-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain (unp residues 156-453)	Not recorded	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Bis Tris 0.1M, lithium sulfate 1.6M and magnesium sulfate 50 mM , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.44 Å R-free 0.260
4IA2 Diastereotopic and Deuterium Effects in Gemini Deposited 2012-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain (unp residues 156-453)	Not recorded	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.95 Å R-free 0.256
4IA3 Diastereotopic and Deuterium Effects in Gemini Deposited 2012-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain (unp residues 156-453)	Not recorded	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.260
4IA7 Diastereotopic and Deuterium Effects in Gemini Deposited 2012-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa） Fragment：Ligand binding domain (unp residues 156-453)	Not recorded	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.255
4Q0A Vitamin D Receptor complex with lithocholic acid Deposited 2014-04-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 156–453（298 aa） Fragment：Ligand binding domain	Not recorded	4OA (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；BTP 0.1M, NaOAc 3M, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.90 Å R-free 0.244
4RUJ Crystal structure of zVDR L337H mutant-VD complex Deposited 2014-11-20	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 156–453（298 aa） Fragment：ligand binding domain, UNP residues 156-453	Mutation：L337H	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297 K；50 mM BIS-TRIS pH6.5, 1.6 M lithium sulfate, 50 mM magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.35 Å R-free 0.255
4RUO Crystal structure of zVDR L337H mutant-gemini complex Deposited 2014-11-21	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 X 156–453（298 aa） Fragment：ligand binding domain, UNP residues 156-453	Mutation：L337H	BIV 21-NOR-9,10-SECOCHOLESTA-5,7,10(19)-TRIENE-1,3,25-TRIOL, 20-(4-HYDROXY-4-METHYLPENTYL)-, (1A,3B,5Z,7E) × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.81 Å R-free 0.261
4RUP Crystal structure of zVDR L337H mutant-Gemini72 complex Deposited 2014-11-21	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 156–453（298 aa） Fragment：ligand binding domain, UNP residues 156-453	Mutation：L337H	H97 (1R,3R,7E,17beta)-17-[(1R)-6,6,6-trifluoro-5-hydroxy-1-(4-hydroxy-4-methylpentyl)-5-(trifluoromethyl)hex-3-yn-1-yl]-9,1 0-secoestra-5,7-diene-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；Bis-Tris 0.1 M, lithium sulfate 1.6 M and magnesium sulfate 50 mM, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.75 Å R-free 0.253
5E7V Potent Vitamin D Receptor Agonist Deposited 2015-10-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	M7E 1-ALPHA-HYDROXY-27-NOR-25-O-CARBONYL-VITAMIN D3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；li sulfate	Resolution 2.40 Å R-free 0.213
5LGA Structural analysis and biological activities of BXL0124, a Gemini analog of Vitamin D Deposited 2016-07-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	6VH (1~{R},3~{S},5~{Z})-5-[2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(6~{R})-1,1,1-tris(fluoranyl)-10-methyl-2,10-bis(oxidanyl)-2-(trifluoromethyl)undeca-3,8-diyn-6-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；50 mM BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.50 Å R-free 0.241
5MX7 1a,20S-dihydroxyvitamin D3 VDR complex Deposited 2017-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A1 156–453（298 aa） Fragment：UNP residues 156-453	Not recorded	D3V 1a,20S-dihydroxyvitamin D3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 1.98 Å R-free 0.225
5NMA Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain Deposited 2017-04-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	9CW (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{S},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；0.1 M BTP pH 7.0, 3 M NaOAc	Resolution 2.80 Å R-free 0.272
5NMB Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain Deposited 2017-04-05	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A2 156–453（298 aa） Fragment：UNP residues 156-453	Not recorded	9CZ (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{S},5~{R})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；0.1 M BTP pH 7.0, 3 M NaOAc	Resolution 2.50 Å R-free 0.260
5OW7 VDR complex Deposited 2017-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	AYK (3~{S})-3-[(1~{S},3~{a}~{S},4~{E},7~{a}~{S})-7~{a}-methyl-4-[(2~{Z})-2-[(5~{S})-2-methylidene-5-oxidanyl-cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-3-oxidanyl-~{N}-propan-2-yl-butanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.10 Å R-free 0.227
5OW9 Vitamin D receptor complex Deposited 2017-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	AYT (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-[(2~{S})-6-methyl-2-oxidanyl-heptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.40 Å R-free 0.246
5OWD Vitamin D receptor complex Deposited 2017-08-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	B0B (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-[(2~{S})-6-methyl-2-oxidanyl-hept-5-en-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.15 Å R-free 0.219
6FO7 Vitamin D nuclear receptor complex 3 Deposited 2018-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	LX3 (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hept-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.59 Å R-free 0.230
6FO8 Vitamin D nuclear receptor complex 4 Deposited 2018-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain 1 156–453（298 aa）	Not recorded	DZT (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]non-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.30 Å R-free 0.235
6FO9 Vitamin D nuclear receptor complex 2 Deposited 2018-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	E0E (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]hex-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.70 Å R-free 0.225
6FOB Vitamin D receptor complex 5 Deposited 2018-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	DZW (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]dec-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.75 Å R-free 0.229
6FOD Vitamin D nuclear receptor complex 1 Deposited 2018-02-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	E05 (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.50 Å R-free 0.244
6T2M VDR-ZK168281 complex Deposited 2019-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	M9Q ethyl (~{Z})-3-[1-[(~{E},1~{R},4~{R})-4-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[(2~{Z})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-oxidanyl-pent-2-enyl]cyclopropyl]prop-2-enoate × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 3.00 Å R-free 0.259
6XZH Structure of zVDR LBD-Calcitriol in complex with chimera 10 Deposited 2020-02-04	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 156–453（298 aa）	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；Sodium acetate 2.5 M, Hepes 100 mM	Resolution 2.37 Å R-free 0.282
6XZI Structure of zVDR LBD-calcitriol in complex with chimera 11 Deposited 2020-02-04	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 156–453（298 aa）	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；NH4Acetate 3.5M, 0.1 M Tris pH 8	Resolution 2.10 Å R-free 0.212
6XZJ Structure of zVDR LBD-Calcitriol in complex with chimera 12 Deposited 2020-02-04	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 156–453（298 aa）	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；NaAcetate 3M, 0.1 M Tris pH 7.5	Resolution 2.10 Å R-free 0.247
6XZK Structure of zVDR LBD-Calcitriol in complex with chimera 13 Deposited 2020-02-04	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 156–453（298 aa）	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；Lithium sulfate 1.8 M, Mes 100 mM	Resolution 2.00 Å R-free 0.224
6XZV Structure of zVDR LBD-Calcitriol in complex with chimera 18 Deposited 2020-02-05	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 156–453（298 aa）	Not recorded	VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；290 K；Lithium sulfate 1.5 M	Resolution 2.30 Å R-free 0.231
7B39 Allene-Based Design of a Noncalcemic Vitamin D Receptor Agonist Deposited 2020-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	T0H (1R,3S,Z)-5-(2-((3aS,7aS,E)-1-(6-hydroxy-6-methylhept-1-en-1-ylidene)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-4-methylenecyclohexane-1,3-diol × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50 mM BisTris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.13 Å R-free 0.247
7BNS VDR complex with BXL-62 Deposited 2021-01-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A2 156–453（298 aa）	Not recorded	U5W 1,25-Dihydroxy-16-ene-20-cyclopropyl-vitamin D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；273 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.70 Å R-free 0.260
7BNU VDR complex with BXL-62 Deposited 2021-01-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A2 156–453（298 aa）	Not recorded	U5W 1,25-Dihydroxy-16-ene-20-cyclopropyl-vitamin D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；273 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.40 Å R-free 0.261
7BO6 VDR complex with LCA derivative Deposited 2021-01-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	FKC (4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.86 Å R-free 0.263
7OXU VDR complex - calcitroic acid Deposited 2021-06-23	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 156–453（298 aa）	Not recorded	2QI calcitroic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M Mes pH 6 and 1.8 M lithium sulfate	Resolution 2.39 Å R-free 0.259
7OXZ VDR complex with a side-chain hydroxylated derivative of lithocholic acid Deposited 2021-06-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	2UI (3R,6R)-6-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]heptane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.20 Å R-free 0.254
7OY4 VDR complex of a side-chain hydroxylated derivatives of lithocholic acid Deposited 2021-06-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	2WV (3S,6R)-6-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]heptane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.00 Å R-free 0.238
7ZFG VDR complex with aromatic D-ring analog Deposited 2022-04-01	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 IV5 (1R,3S,5Z)-4-methylidene-5-[(E)-9-methyl-3-[3-(6-methyl-6-oxidanyl-heptyl)phenyl]-9-oxidanyl-dec-2-enylidene]cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；NaAcetate 2.5M, BisTris 0.1M	Resolution 2.62 Å R-free 0.261
7ZFX VDR complex with Aromatic-D-Ring Analog Deposited 2022-04-01	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 IV1 (1R,3S,5Z)-5-[(E)-3-[3,5-bis(6-methyl-6-oxidanyl-heptyl)phenyl]prop-2-enylidene]-4-methylidene-cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；NaActetae 2.5M, Tris 0.1M	Resolution 2.60 Å R-free 0.254
8CK5 VDR LBD complex with 25-nitro derivative of 1,25D3 Deposited 2023-02-14	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 UYO (1S,3R,5Z,7E,13xi)-25-nitro-9,10-secocholesta-5,7,10-triene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.10 Å R-free 0.243
8CKC Vitamin D receptor complex with 25-amine derivative of 1,25D3 Deposited 2023-02-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 UYU (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R)-6-azanyl-6-methyl-heptan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate	Resolution 2.10 Å R-free 0.232
8P9W vitamin D receptor complex with Xe4MeCF3 analog Deposited 2023-06-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	XDO (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-1,7~{a}-dimethyl-1-[6,6,6-tris(fluoranyl)-5-oxidanyl-5-(trifluoromethyl)hexa-1,3-diynyl]-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BTP pH 7.0, 3 M NaOAc	Resolution 2.90 Å R-free 0.234
8P9X Vitamin D receptor complex with Xe4Me agonist ligand Deposited 2023-06-06	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 FO6 (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-1,7~{a}-dimethyl-1-(5-methyl-5-oxidanyl-hexa-1,3-diynyl)-2,3,3~{a},5,6,7-hexahydroinden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BTP pH 7.0, 3 M NaOAc	Resolution 2.15 Å R-free 0.241
8PWD Crystal structure of VDR in complex Des-C-Ring and Aromatic-D-Ring analog 3c Deposited 2023-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	FT9 (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；NH4SO4 1.5M, BisTris 0.1M pH 7	Resolution 2.80 Å R-free 0.274
8PWE Crystal structure of VDR complex with Novel Des-C-Ring and Aromatic-D-Ring analog 3a Deposited 2023-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 FUW (1~{R},3~{S},5~{Z})-4-methylidene-5-[(~{E})-3-[3-(6-methyl-6-oxidanyl-hept-3-ynyl)phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；NaAcetate 2.5M, BisTris 0.1M pH 7	Resolution 2.00 Å R-free 0.233
8PWF crystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 2 Deposited 2023-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	FVB (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)heptyl]phenyl]pent-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；LiSO4 1.6M, Hepes 0.1M pH 7.5	Resolution 2.30 Å R-free 0.265
8PWM Crystal structure of VDR in complex with Des-C-Ring and Aromatic-D-Ring analog 3b Deposited 2023-07-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 HXI (1R,3S,5Z)-4-methylidene-5-[(E)-3-[3-[7,7,7-tris(fluoranyl)-6-oxidanyl-6-(trifluoromethyl)hept-3-ynyl]phenyl]but-2-enylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；NaAcetate 2.5M, BisTris 0.1M pH 7	Resolution 2.30 Å R-free 0.252
8PZ6 crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 analog 56 Deposited 2023-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	IG5 (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{S},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,6,7,8,9,9~{a}-octahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-(3-oxidanylpropylidene)cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NaAcetate 3M, Hepes 0.1M pH 7.5	Resolution 2.90 Å R-free 0.292
8PZ7 crystal structure of VDR complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 57 Deposited 2023-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	IG0 (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methyl-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；NH4Acetate 3.5M, BisTrisPropane 0.1M pH 7	Resolution 2.93 Å R-free 0.257
8PZ8 crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 54 Deposited 2023-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	IFU (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{S},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,6,7,8,9,9~{a}-octahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；(NH4)2SO4 1.5M	Resolution 2.64 Å R-free 0.261
8PZ9 Crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 55 Deposited 2023-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	IFK (1~{R},3~{R})-5-[(2~{E})-2-[(4~{a}~{R},5~{R},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,8,9,9~{a}-hexahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；NaAcetate 3M, Hepes 0.1M pH 7.5	Resolution 2.74 Å R-free 0.278
8PZB crystal structure of VDR in complex with D-Bishomo-1a,25-dihydroxyvitamin D3 Analog 49 Deposited 2023-07-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	I72 (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(4~{a}~{R},5~{S},9~{a}~{S})-4~{a}-methyl-5-[(2~{R})-6-methyl-6-oxidanyl-heptan-2-yl]-3,4,5,6,7,8,9,9~{a}-octahydro-2~{H}-benzo[7]annulen-1-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；(NH4)2SO4 1.6M, Mes 0.1M pH 6	Resolution 2.73 Å R-free 0.275
9EYR VDR complex with gemini analog UG-480 Deposited 2024-04-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1H75 (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{R})-5-methyl-1-[(1~{S},2~{S})-2-(3-methyl-3-oxidanyl-butyl)cyclopropyl]-5-oxidanyl-hexyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Li2SO4 1.8M	Resolution 2.56 Å R-free 0.259
9EZ1 Vitamin D receptor in complex with 1,4a,25-trihydroxyvitamin D3 Deposited 2024-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1H9P 1,4a,25-trihydroxyvitamin D3 × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES pH 6.0,2.5 M NaOAc	Resolution 1.95 Å R-free 0.258
9EZ2 Vitamin D receptor complex with 1,4b,25-trihydroxyvitamin D3 Deposited 2024-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1H72 1,4b,25-trihydroxyvitamin D3 × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES pH 6.0,2.5 M NaOAc	Resolution 1.80 Å R-free 0.230
9FBF VDR complex with UG-481 Deposited 2024-05-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1IBM (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-5-methyl-1-[(1~{R},2~{R})-2-(3-methyl-3-oxidanyl-butyl)cyclopropyl]-5-oxidanyl-hexyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Li2SO4 1.8M	Resolution 3.01 Å R-free 0.258
9FW8 VDR complex with UG-650 Deposited 2024-06-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1IGV (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{S})-7-methyl-4-methylidene-7-oxidanyl-octan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；(NH4)2SO4 1.5 M, BisTris 0.1 M pH 7	Resolution 2.42 Å R-free 0.261
9GY8 Vitamin D Receptor complex with Sila-A Deposited 2024-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	A1IQM (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-5-trimethylsilylpentan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；(NH4)2SO4 1.5M, Tris 0.1M pH 8	Resolution 2.20 Å R-free 0.262
9GYA Vitamin D Receptor in complex with Sila-e Deposited 2024-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 A1IQQ (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-dimethylsilylpent-4-yn-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；NaAcetate 2.5M, Hepes 0.1M pH 7.5	Resolution 1.85 Å R-free 0.232
9GYC Vitamin D receptor in complex with Sila-d Deposited 2024-10-01	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 A1IQP (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5-[~{tert}-butyl(dimethyl)silyl]pent-4-yn-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；NaAcetate 2.5M, Hepes 0.1M pH 7.5	Resolution 2.20 Å R-free 0.246
9GYJ Vitamin D receptor in complex with Sila-c Deposited 2024-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 A1IQN (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-5-trimethylsilylpent-4-yn-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；NaAcetate 2.5M	Resolution 1.90 Å R-free 0.239
9GYK Vitamin D receptor in complex with Sila-f Deposited 2024-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 156–453（298 aa）	Not recorded	ACT ACETATE ION × 2 A1IQO (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{S},3~{a}~{S},7~{a}~{S})-7~{a}-methyl-1-(4-trimethylsilylbuta-1,3-diynyl)-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；NaAcetate 2.5M, Hepes 0.1M pH 7.5	Resolution 2.20 Å R-free 0.255
9RAP VDR complex with UG-635 Deposited 2025-05-21	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 156–453（298 aa）	Not recorded	ACT ACETATE ION × 1 A1JD0 (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{S})-6-[bis(oxidanyl)amino]-6-methyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；3M Na Acetate 0.1M Tris HCl pH8	Resolution 2.20 Å R-free 0.249
9RCG Vitamin D receptor complex with a vitamin D receptor agonist/histone deacetylase inhibitor hybrid molecule Deposited 2025-05-28	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 156–453（298 aa）	Not recorded	A1JD5 4-[4-[3-[5-[(3~{S})-4,4-dimethyl-3-oxidanyl-pentyl]-4-methyl-1,3-thiazol-2-yl]pentan-3-yl]phenoxy]-~{N}-oxidanyl-butanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Na2 Tartrate 1.1M, MgCl2 0.2M, Hepes 0.1M pH7.5	Resolution 2.10 Å R-free 0.206

74 other PDB entries and 74 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VDRA_DANRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–302； UniProt 156–453

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	5nky
Deposition date deposition_date	2017-04-03
Structure title title	Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain
Keywords keywords	GENE REGULATION; GENE REGULATION
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	19.17 Å
Radius of gyration Rg (electron density) rg_electron	17.81 Å
Forward intensity I(0) i0	13808200.00
Molecular weight molecular_weight	28708.0 kDa
Excluded volume excluded_volume	36361 Å³
Envelope volume envelope_volume	40877 Å³
Hydration-shell volume shell_volume	18957 Å³
Envelope diameter envelope_diameter	63.8 Å
Shell Rg shell_rg	24.34 Å
Envelope Rg envelope_rg	18.13 Å
Shape Rg shape_rg	17.78 Å
Total Rg total_rg	18.91 Å
Total atoms total_atoms	2017
Residues n_residues	248
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	61.8 Å
Rg (real space) rg_real	19.05 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	1.3810e+07
I(0) uncertainty (real space) i0_real_error	1.8030e+05
Rg (reciprocal space) rg_reciprocal	19.07 Å
I(0) (reciprocal space) i0_reciprocal	13810000.0000
Solution quality estimate total_estimate	0.8059
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.188
Kurtosis Kurtosis kurtosis	-0.309
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2886000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Vitamin D3 receptor A
Molecular weight formula_weight	34060.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2032

GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS

来源 Source

来源生物 organism	Danio rerio
通用名 common_name	Zebrafish
NCBI Class编号 ncbi_taxonomy_id	7955
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SRC1
Molecular weight formula_weight	1776.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

RHKILHRLLQEGSPS

Entity 3 Entity 3 non-polymer

Description description	;(1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(1~{S})-1-[(2~{R},5~{S})-5-(2-oxidanylpropan-2-yl)oxolan-2-yl]ethyl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol ;
Molecular weight formula_weight	444.6 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	15

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	5nkyA00
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	66.191 Å
Unit-cell length b length_b	66.191 Å
Unit-cell length c length_c	261.698 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.096 Å
Low-resolution limit resolution_low	43.616 Å
R factor r_factor	0.2272
R_work r_work	0.2262
R_free r_free	0.2463

fit	/app/data/saxs_computation/nk/5nky/5nky.fit
pddf	/app/data/pr_computation/nk/5nky/5nky.pr.out
profile	/app/data/saxs_computation/nk/5nky/5nky.dat

Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain

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

Vitamin D3 receptor A

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) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)