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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 169–475 | 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 |
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 5V39 | 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
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 |
| 1KB6 Crystal Structure of VDR DNA-binding Domain Bound to Rat Osteocalcin (OC) Response Element Deposited 2001-11-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric |
Chain A
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 0.275 |
| 1S0Z Crystal structure of the VDR LBD complexed to seocalcitol. Deposited 2004-01-05 | Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 mutation/modification 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 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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 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 mutation/modification 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 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 mutation/modification 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 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 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 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 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 mutation/modification 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 |
| 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 | P11473-2 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–256； UniProt 169–475 |
