1kb6

Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element

Method: X-RAY DIFFRACTION D_max: 80.3 Å Quality: REASONABLE

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

Vitamin D3 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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 16–125 Chain B； UniProt 16–125	Fragment：DNA-binding Domain (Residues 16-125)	5'-D(CPAPCPGPGPGPTPGPAPAPTPGPAPGPGPAPCPA)-3' × 1 5'-D(TPGPTPCPCPTPCPAPTPTPCPAPCPCPCPGPTPG)-3' × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.275

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 1KB6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DB1 CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D Deposited 1999-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：LIGAND BINDING DOMAIN Chain A 216–427（212 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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；ammonium sulfate, mes, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.214
1IE8 Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to KH1060 Deposited 2001-04-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Chain A 216–427（212 aa）	Not recorded	KH1 5-(2-{1-[1-(4-ETHYL-4-HYDROXY-HEXYLOXY)-ETHYL]-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 6；277 K；Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.52 Å R-free 0.230
1IE9 Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to MC1288 Deposited 2001-04-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Chain A 216–427（212 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 6；277 K；Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.40 Å R-free 0.248
1KB2 Crystal Structure of VDR DNA-binding Domain Bound to Mouse Osteopontin (SPP) Response Element Deposited 2001-11-05	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 16–125（110 aa） Fragment：DNA-binding Domain (Residues 16-125) Chain B 16–125（110 aa） Fragment：DNA-binding Domain (Residues 16-125)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.289
1KB4 Crystal Structure of VDR DNA-binding Domain Bound to a Canonical Direct Repeat with Three Base Pair Spacer (DR3) Response Element Deposited 2001-11-05	Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 16–125（110 aa） Fragment：DNA-binding Domain (Residues 16-125) Chain B 16–125（110 aa） Fragment：DNA-binding Domain (Residues 16-125)	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；PEG 8000, magnesium chloride, MES, glycerol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.272
1S0Z Crystal structure of the VDR LBD complexed to seocalcitol. Deposited 2004-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：VDR ligand binding domain Chain A 216–427（212 aa） Fragment：VDR ligand binding domain	Not recorded	EB1 SEOCALCITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.204
1S19 Crystal structure of VDR ligand binding domain complexed to calcipotriol. Deposited 2004-01-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：VDR ligand binding domain Chain A 216–427（212 aa） Fragment：VDR ligand binding domain	Not recorded	MC9 CALCIPOTRIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.214
1TXI Crystal structure of the vdr ligand binding domain complexed to TX522 Deposited 2004-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain Chain A 216–427（212 aa） Fragment：ligand binding domain	Not recorded	TX5 (1R,3R)-5-((Z)-2-((1R,7AS)-HEXAHYDRO-1-((S)-6-HYDROXY-6-METHYLHEPT-4-YN-2-YL)-7A-METHYL-1H-INDEN-4(7AH)-YLIDENE)ETHYLIDENE)CYCLOHEXANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.218
1YNW Crystal Structure of Vitamin D Receptor and 9-cis Retinoic Acid Receptor DNA-Binding Domains Bound to a DR3 Response Element Deposited 2005-01-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 16–125（110 aa） Fragment：DNA-binding Domain (Residues 16-125)	Mutation：P61A,F62A,H75A	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；PEG 8000, ammonium citrate, Tris, glycerol, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.283
2HAM Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol Deposited 2006-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand binding domain Chain A 216–427（212 aa） Fragment：Ligand binding domain	Not recorded	C33 2ALPHA-PROPYL-1ALPHA,25-DIHYDROXYVITAMIN D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.216
2HAR Crystal structure of VDR LBD in complex with 2 alpha-(3-hydroxy-1-propoxy) calcitriol Deposited 2006-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand binding domain Chain A 216–427（212 aa） Fragment：Ligand binding domain	Not recorded	OCC 2ALPHA-(3-HYDROXYPROPOXY)-1ALPHA,25-DIHYDROXYVITAMIN D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.227
2HAS Crystal structure of VDR LBD in complex with 2alpha-(1-propoxy) calcitriol Deposited 2006-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain Chain A 216–427（212 aa） Fragment：ligand binding domain	Not recorded	C3O 2ALPHA-PROPOXY-1ALPHA,25-DIHYDROXYVITAMIN D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.96 Å R-free 0.228
2HB7 Crystal structure of VDR LBD in complex with 2alpha(3-hydroxy-1-propyl) calcitriol Deposited 2006-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand binding domain Chain A 216–427（212 aa） Fragment：Ligand binding domain	Not recorded	O1C 2ALPHA-(3-HYDROXYPROPYL)-1ALPHA,25-DIHYDROXYVITAMIN D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.204
2HB8 Crystal structure of VDR LBD in complex with 2alpha-methyl calcitriol Deposited 2006-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand binding domain Chain A 216–427（212 aa） Fragment：Ligand binding domain	Not recorded	MVD 2ALPHA-METHYL-1ALPHA,25-DIHYDROXY-VITAMIN D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Ammonium sulphate 1.4M, Mes 0.1M, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.224
3A2I Crystal structure of the human vitamin D receptor (H305F) ligand binding domain complexed with TEI-9647 Deposited 2009-05-20	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 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：H305F, DEL(165-215) mutant Mutation：H305F, DEL(165-215) mutant	TEJ (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, pH 6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.27 Å R-free 0.276
3A2J Crystal structure of the human vitamin D receptor (H305F/H397F) ligand binding domain complexed with TEI-9647 Deposited 2009-05-20	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 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：H305F, H397F, DEL(165-215) mutant Mutation：H305F, H397F, DEL(165-215) mutant	TEJ (1S,3R,5Z,7E,20S,23S)-1,3-dihydroxy-23,26-epoxy-9,10-secocholesta-5,7,10,25(27)-tetraen-26-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, pH 6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.267
3A3Z Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277A(C23S) Deposited 2009-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 118–427（310 aa） Fragment：Ligand Binding Domain, UNP residues 118-427	Not recorded	2MV (1S,2S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-2-methyl-9,10-secoandrosta-5,7,10-triene-1,3-diol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；10mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.72 Å R-free 0.209
3A40 Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R) Deposited 2009-06-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 118–427（310 aa） Fragment：Ligand Binding Domain, UNP residues 118-427	Not recorded	23R (1S,2S,3R,5Z,7E,14beta,17alpha,23R)-23-(2-hydroxy-2-methylpropyl)-2-methyl-20,24-epoxy-9,10-secochola-5,7,10-triene-1,3-diol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；10mM Tris, 100mM NaCl, 1nM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.45 Å R-free 0.196
3A78 Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3 Deposited 2009-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand Binding Domain Chain A 216–427（212 aa） Fragment：Ligand Binding Domain	Not recorded	3EV (1S,3S,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；10mM Tris, 100mM NaCl, 1mM TCEP, 0.05M Mes, 0.7M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.203
3AUQ Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2alpha-methyl-19-norvitamin D3 Deposited 2011-02-15	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 118–164（47 aa） Fragment：ligand binding domain Chain A 216–427（212 aa） Fragment：ligand binding domain	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	CA9 (1R,2S,3R)-5-[2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-1,2,3,3a,6,7-hexahydroinden-4-yl]ethynyl]-2-methyl-cyclohex-4-ene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.64 Å R-free 0.286
3AUR Crystal structure of the human vitamin D receptor ligand binding domain complexed with Yne-diene type analog of active 14-epi-2beta-methyl-19-norvitamin D3 Deposited 2011-02-15	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 118–164（47 aa） Fragment：ligand binding domain Chain A 216–427（212 aa） Fragment：ligand binding domain	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	CA9 (1R,2S,3R)-5-[2-[(1R,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-7a-methyl-1,2,3,3a,6,7-hexahydroinden-4-yl]ethynyl]-2-methyl-cyclohex-4-ene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.21 Å R-free 0.254
3AX8 Crystal structure of the human vitamin D receptor ligand binding domain complexed with 15alpha-methoxy-1alpha,25-dihydroxyvitamin D3 Deposited 2011-03-30	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 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	EIM (1R,3S,5Z)-5-[(2E)-2-[(1R,3S,3aS,7aR)-1-[(2R)-6-hydroxy-6-methyl-heptan-2-yl]-3-methoxy-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.294
3AZ1 Crystal Structure Analysis of Vitamin D receptor Deposited 2011-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	DS2 {4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 6；277 K；pH 6.0, hanging drop, temperature 277K	Resolution 1.50 Å R-free 0.213
3AZ2 Crystal Structure Analysis of Vitamin D receptor Deposited 2011-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	DS3 5-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；hanging drop	Resolution 1.69 Å R-free 0.212
3AZ3 Crystal Structure Analysis of Vitamin D receptor Deposited 2011-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	DS6 (4S)-4-hydroxy-5-[4-(3-{4-[(3S)-3-hydroxy-4,4-dimethylpentyl]-3-methylphenyl}pentan-3-yl)-2-methylphenoxy]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；hanging drop	Resolution 1.36 Å R-free 0.243
3B0T Human VDR ligand binding domain in complex with maxacalcitol Deposited 2011-06-14	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 120–164（45 aa） Fragment：vitamin D receptor binding domain Chain A 216–423（208 aa） Fragment：vitamin D receptor binding domain	Mutation：Lack of UNP residues 165-215 Mutation：Lack of UNP residues 165-215	MCZ (1S,3R,5Z,7E,14beta,17alpha,20S)-20-(3-hydroxy-3-methylbutoxy)-9,10-secopregna-5,7,10-triene-1,3-diol × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；0.1M Mes (pH5.5), 1.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.30 Å R-free 0.199
3CS4 Structure-based design of a superagonist ligand for the vitamin D nuclear receptor Deposited 2008-04-09	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 118–427（310 aa） Fragment：UNP residues 118-427	Not recorded	COV (1S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-9,10-secoandrosta-5,7,10-triene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM Mes-KOH and 1.4 M ammonium sulphate at pH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.217
3CS6 Structure-based design of a superagonist ligand for the vitamin D nuclear receptor Deposited 2008-04-09	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 118–427（310 aa） Fragment：UNP residues 118-427	Not recorded	0CO (1S,3R,5Z,7E,14beta,17alpha,23R)-23-(2-hydroxy-2-methylpropyl)-20,24-epoxy-9,10-secochola-5,7,10-triene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100 mM Mes-KOH and 1.4 M ammonium sulphate at pH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.206
3KPZ Crystal structure of a novel vitamin D3 analogue, ZK203278 showing dissociated profile Deposited 2009-11-17	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 118–427（310 aa） Fragment：Ligand binding domain, residues 118-427	Mutation：deletion in residues 166-216	ZNE (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,5S)-5-hydroxy-1-methyl-5-(1,3-thiazol-2-yl)pentyl]-7a-methyloctahydro-4H-inden-4-ylidene}ethylidene]-4-methylidenecyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；273 K；Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 1.90 Å R-free 0.228
3M7R Crystal structure of VDR H305Q mutant Deposited 2010-03-17	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 120–423（304 aa） Fragment：VDR, UNP residues 120-423	Mutation：H305Q	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 6.5；293 K；NH4Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.241
3OGT Design, Chemical synthesis, Functional characterization and Crystal structure of the sidechain analogue of 1,25-dihydroxyvitamin D3. Deposited 2010-08-17	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 118–427（310 aa）	Not recorded	FMV (1S,3R,5Z,7E,14beta,17alpha,20S)-20-[5-(1-hydroxy-1-methylethyl)furan-2-yl]-9,10-secopregna-5,7,10-triene-1,3-diol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES pH6.0, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.184
3P8X Synthesis, Structure, and Biological Activity of des-Side Chain Analogues of 1alpha,25-Dihydroxyvitamin D3 with Substituents at C-18 Deposited 2010-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：Ligand binding domain Chain A 217–427（211 aa） Fragment：Ligand binding domain	Not recorded	ZYD (1R,3S,5Z)-5-{(2E)-2-[(3aR,7aS)-7a-(7-hydroxy-7-methyloctyl)octahydro-4H-inden-4-ylidene]ethylidene}-4-methylidenecyclohexane-1,3-diol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；NH4 sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.209
3TKC Design, Synthesis, Evaluation and Structure of Vitamin D Analogues with Furan Side Chains Deposited 2011-08-26	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 118–427（310 aa）	Not recorded	FMV (1S,3R,5Z,7E,14beta,17alpha,20S)-20-[5-(1-hydroxy-1-methylethyl)furan-2-yl]-9,10-secopregna-5,7,10-triene-1,3-diol × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M MES pH6.0, 1.4 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.183
3VHW Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP Deposited 2011-09-08	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 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	VHW methyl (1S,3E)-3-{(2R)-2-[(1R,3aS,4E,7aR)-4-{(2Z)-2-[(3R,4S,5R)-3,5-dihydroxy-4-(3-hydroxypropoxy)-2-methylidenecyclohexylidene]ethylidene}-7a-methyloctahydro-1H-inden-1-yl]propylidene}-1-ethyl-2-oxocyclopentanecarboxylate (non-preferred name) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.43 Å R-free 0.247
3W0A Crystal Structure Analysis of Vitamin D receptor Deposited 2012-10-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	DS5 (4S)-4-hydroxy-5-[2-methyl-4-(3-{3-methyl-4-[4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-yn-1-yl]phenyl}pentan-3-yl)phenoxy]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 1.80 Å R-free 0.236
3W0C Crystal Structure Analysis of Vitamin D receptor Deposited 2012-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	6DS (4S)-4-hydroxy-5-[2-methyl-4-(3-{3-methyl-4-[(1E)-4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-en-1-yl]phenyl}pentan-3-yl)phenoxy]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.235
3W0Y Crystal Structure Analysis of Vitamin D receptor Deposited 2012-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 120–164（45 aa） Fragment：UNP RESIDUES 120-164, 216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 120-164, 216-423	Not recorded	DS4 [3-fluoro-2'-methyl-4'-(3-{3-methyl-4-[(1E)-4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-en-1-yl]phenyl}pentan-3-yl)biphenyl-4-yl]acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；277 K；pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.98 Å R-free 0.218
3WGP Crystal Structure Analysis of Vitamin D receptor Deposited 2013-08-07	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 120–423（304 aa） Fragment：UNP residues 120-423	Not recorded	ED9 (1R,2R,3R,5Z,7E,14beta,17alpha)-2-(3-hydroxypropoxy)-9,10-secocholesta-5,7,10-triene-1,3,25-triol × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.207
3WWR Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1-((((1S,2R,6R,Z)-2,6-dihydroxy-4-((E)-2-((1R,3aS,7aR)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methylhexahydro-1H-inden-4(2H)-ylidene)ethylidene)-3-methylenecyclohexyl)oxy)methyl)cyclopropanecarbonitrile Deposited 2014-06-27	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 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：DELETION (165-215) mutantion Mutation：DELETION (165-215) mutantion	3AJ 1-({[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}methyl)cyclopropanecarbonitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293K	Resolution 3.18 Å R-free 0.291
3X31 Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-14-epi-1a,25-Dihydroxy-19-norvitamin D3 Deposited 2015-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain (UNP residues 118-164, 216-427) Chain A 216–427（212 aa） Fragment：ligand binding domain (UNP residues 118-164, 216-427)	Not recorded	41V (1R,3R,7Z,14beta,17alpha)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293K, temperature 293.0K	Resolution 2.11 Å R-free 0.299
3X36 Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-1a,25-Dihydroxy-19-norvitamin D3 Deposited 2015-01-16	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 118–164（47 aa） Fragment：ligand binding domain (UNP residues 118-164, 216-427) Chain A 216–427（212 aa） Fragment：ligand binding domain (UNP residues 118-164, 216-427)	Mutation：DELETION (165-215) mutantion Mutation：DELETION (165-215) mutantion	41W (1R,3R)-5-[(2Z)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K	Resolution 1.93 Å R-free 0.221
4G2I Structural basis for the accommodation of bis- and tris-aromatic derivatives in Vitamin D Nuclear Receptor Deposited 2012-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–427（310 aa） Fragment：unp residues 118-417	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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M Mes and 1.4 M ammonium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.223
4ITE Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(2H-tetrazol-2-yl)ethyl]vitamin D3 Deposited 2013-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	TEY (1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-2-yl)ethyl]cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.49 Å R-free 0.248
4ITF Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1alpha,25-Dihydroxy-2alpha-[2-(1H-tetrazole-1-yl)ethyl]vitamin D3 Deposited 2013-01-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain, residues 118-427 Chain A 216–427（212 aa） Fragment：ligand binding domain, residues 118-427	Mutation：DEL(165-215) mutant Mutation：DEL(165-215) mutant	TFY (1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-2-[2-(1,2,3,4-tetrazol-1-yl)ethyl]cyclohexane-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.84 Å R-free 0.255
5GT4 Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R,5Z,7E,14beta,17alpha)-2-cyanopropoxy-9,10-secocholesta-5,7,10-triene-1,3,25-triol Deposited 2016-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：UNP RESIDUES 118-164,216-423 Chain A 216–423（208 aa） Fragment：UNP RESIDUES 118-164,216-423	Not recorded	2KB 4-{[(1R,2S,3R,5Z,7E,14beta,17alpha)-1,3,25-trihydroxy-9,10-secocholesta-5,7,10-trien-2-yl]oxy}butanenitrile × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；277 K；50mM Mes, 1.4M ammonium sulphate	Resolution 1.83 Å R-free 0.217
5V39 Crystal structure of human vitamin D receptor ligand binding domain in complex with a VDRM Deposited 2017-03-06	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 169–475（307 aa）	Not recorded	8VM 5-(3-{4-[(2S)-2-hydroxy-3,3-dimethylbutoxy]-3-methylphenyl}pentan-3-yl)-3-methyl-N-(1H-tetrazol-5-yl)thiophene-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；100mM Tris HCl pH 8.5, 25% PEG 3350 and 200mM Ammonium Sulfate	Resolution 2.20 Å R-free 0.235
5YSY Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol Deposited 2017-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain Chain A 216–423（208 aa） Fragment：ligand binding domain	Not recorded	90L (1R,2R,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]e thenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50mM Mes, 1.4M ammonium sulphate	Resolution 2.00 Å R-free 0.242
5YT2 Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol Deposited 2017-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–164（47 aa） Fragment：ligand binding domain Chain A 216–423（208 aa） Fragment：ligand binding domain	Not recorded	90O (1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；50mM Mes, 1.4M ammonium sulphate	Resolution 2.00 Å R-free 0.233
7QPP High resolution structure of human VDR ligand binding domain in complex with calcitriol Deposited 2022-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–165（48 aa） Chain A 217–427（211 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 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Ammonium Sulfate, pH 6.0	Resolution 1.52 Å R-free 0.166
8IQN Crystal structure of the human vitamin D receptor ligand binding domain complexed with 24,24-F2-25(OH)D3 Deposited 2023-03-17	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 118–423（306 aa）	Not recorded	SRF (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R})-5,5-bis(fluoranyl)-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES, pH6.5, 1.2-1.6M ammonium sulfate	Resolution 1.64 Å R-free 0.206
8IQT Crystal structure of the human vitamin D receptor ligand binding domain complexed with (23R)-F-25(OH)D3 Deposited 2023-03-17	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 118–423（306 aa）	Not recorded	SV0 (1~{S},3~{Z})-3-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},4~{R})-4-fluoranyl-6-methyl-6-oxidanyl-heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M MES, 1.2-1.6M ammonium sulfate, pH 6.5	Resolution 1.75 Å R-free 0.207

51 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VDR_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 16–125 Author chain B； PDBConstruct 1–110； UniProt 16–125

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	1kb6
Deposition date deposition_date	2001-11-05
Structure title title	Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element
Keywords keywords	VDR, NUCLEAR RECEPTOR, PROTEIN-DNA COMPLEX, VITAMIN D, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	22.00 Å
Radius of gyration Rg (electron density) rg_electron	21.82 Å
Forward intensity I(0) i0	30153400.00
Molecular weight molecular_weight	32987.0 kDa
Excluded volume excluded_volume	37360 Å³
Envelope volume envelope_volume	49455 Å³
Hydration-shell volume shell_volume	19996 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	27.24 Å
Envelope Rg envelope_rg	21.96 Å
Shape Rg shape_rg	21.81 Å
Total Rg total_rg	22.43 Å
Total atoms total_atoms	2237
Residues n_residues	231
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	80.3 Å
Rg (real space) rg_real	22.13 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	3.0150e+07
I(0) uncertainty (real space) i0_real_error	4.6180e+05
Rg (reciprocal space) rg_reciprocal	22.10 Å
I(0) (reciprocal space) i0_reciprocal	30150000.0000
Solution quality estimate total_estimate	0.7432
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.521
Kurtosis Kurtosis kurtosis	-0.048
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4523000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.724; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	5'-D(CPAPCPGPGPGPTPGPAPAPTPGPAPGPGPAPCPA)-3'
Molecular weight formula_weight	5614.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2271

CACGGGTGAATGAGGACA

Entity 2 Entity 2 polymer

Description description	5'-D(TPGPTPCPCPTPCPAPTPTPCPAPCPCPCPGPTPG)-3'
Molecular weight formula_weight	5418.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TGTCCTCATTCACCCGTG

Entity 3 Entity 3 polymer

Description description	Vitamin D3 Receptor
Molecular weight formula_weight	12953.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

FDRNVPRICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKREMILKRKEEEALKDSLRPKLS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kb6a_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d1kb6b_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

CATH v4.4 (2 domains)

Domain ID domain_id	1kb6A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	1kb6B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

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8. Citations (1)

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Unit-cell length a length_a	61.150 Å
Unit-cell length b length_b	61.150 Å
Unit-cell length c length_c	241.800 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2230
R_free r_free	0.2750

fit	/app/data/saxs_computation/kb/1kb6/1kb6.fit
pddf	/app/data/pr_computation/kb/1kb6/1kb6.pr.out
profile	/app/data/saxs_computation/kb/1kb6/1kb6.dat

Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element

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

Vitamin D3 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)