Vitamin D3 receptor
Rattus norvegicus
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 116–423 | Mutation：165-211 deletion | 13-meric peptide from DRIP205 NR2 BOX peptide × 1 9KX (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol | Resolution 2.40 Å R-free 0.228 |
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 5ZWI | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1RJK crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VDZ 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.99 Å R-free 0.244 |
| 1RJK crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VDZ 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIO L × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.99 Å R-free 0.244 |
| 1RK3 crystal structure of the rat vitamin D receptor ligand binding domain complexed with 1,25-dihydroxyvitamin D3 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.243 |
| 1RK3 crystal structure of the rat vitamin D receptor ligand binding domain complexed with 1,25-dihydroxyvitamin D3 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.20 Å R-free 0.243 |
| 1RKG crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VD1 5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.226 |
| 1RKG crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MbisP and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VD1 5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 1.90 Å R-free 0.226 |
| 1RKH crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-21 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VD2 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.28 Å R-free 0.218 |
| 1RKH crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2AM20R and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2003-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：Chain A, DEL(165-211) | VD2 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL-CYCLOHEXANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 4000, MOPS, ammonium citrate, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
|
Resolution 2.28 Å R-free 0.218 |
| 2O4J Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205 Deposited 2006-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：residues Ser165 through Pro211 are deleted from the protein | VD4 (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
macroseeding in batch；pH 7；295 K；PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
|
Resolution 1.74 Å R-free 0.246 |
| 2O4J Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205 Deposited 2006-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：residues Ser165 through Pro211 are deleted from the protein | VD4 (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
macroseeding in batch；pH 7；295 K；PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
|
Resolution 1.74 Å R-free 0.246 |
| 2O4R Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20E and the NR2 Box of DRIP 205 Deposited 2006-12-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：residues Ser165 through Pro211 are deleted from the protein | VD5 (1R,3R,7E,17E)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
macroseeding in batch；pH 7；295 K；PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
|
Resolution 1.98 Å R-free 0.240 |
| 2O4R Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20E and the NR2 Box of DRIP 205 Deposited 2006-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
116–423（308 aa）
Fragment：ligand binding domain
|
Mutation：residues Ser165 through Pro211 are deleted from the protein | VD5 (1R,3R,7E,17E)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-1,3-diol × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
macroseeding in batch；pH 7；295 K；PEG 4000, MOPS, Ammonium Citrate, Isopropanol, pH 7.0, macroseeding in batch, temperature 295K
|
Resolution 1.98 Å R-free 0.240 |
| 2ZFX Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR301 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2008-01-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：ligand binding domain
Chain A
212–423（212 aa）
Fragment：ligand binding domain
|
Mutation：DEL(165-211) mutant Mutation：DEL(165-211) mutant | YR3 (2S)-3-{4-[1-ethyl-1-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propyl]-2-methylphenoxy}propane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.99 Å R-free 0.258 |
| 2ZL9 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure Deposited 2008-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP residues 116-423
|
Not recorded | VDA (1R,2R,3R,5Z)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；0.1-0.4M formic acid, 15-20% polyethylene glycol(PEG)4000, 0-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
|
Resolution 1.90 Å R-free 0.276 |
| 2ZLA 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure Deposited 2008-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP residues 116-423
|
Not recorded | VDB (1R,2S,3R,5Z,7E)-17-{(1R)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethoxy)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1-0.4M formic acid, 15-20% polyethylene glycol(PEG)4000, 0-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.263 |
| 2ZLC 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure Deposited 2008-04-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP residues 116-423
|
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；293 K；0.1-0.4 M formic acid, 15-20% polyethylene glycol(PEG)4000, 0-20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.261 |
| 2ZMH Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism Deposited 2008-04-18 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 116-423
|
Mutation：Deletion UNP residues 165-211 | NYA (1R,3R,7E,17beta)-17-{(1R,2E,4R)-4-hydroxy-1-methyl-4-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]but-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, MOPS, sodium formate, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.268 |
| 2ZMI Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism Deposited 2008-04-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 116-423
|
Mutation：Deletion UNP residues 165-211 | TT2 (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, MOPS, sodium formate, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.222 |
| 2ZMJ Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism Deposited 2008-04-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 116-423
|
Mutation：Deletion UNP residues 165-211 | MI4 (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 4000, MOPS, sodium formate, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.271 |
| 2ZXM A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket Deposited 2009-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-423
|
Not recorded | JB1 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)heptan-2-yl]-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 7；293 K；MOPS-Na, Na-Formate, PEG4000, Ethyleneglycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.01 Å R-free 0.295 |
| 2ZXM A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket Deposited 2009-01-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-423
|
Not recorded | JB1 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)heptan-2-yl]-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 7；293 K；MOPS-Na, Na-Formate, PEG4000, Ethyleneglycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.01 Å R-free 0.295 |
| 2ZXN A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket Deposited 2009-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-423
|
Not recorded | JC1 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S,3S)-3-(2-hydroxyethyl)heptan-2-yl]-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 7；293 K；MOPS-Na, Na-Formate, PEG4000, Ethyleneglycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.251 |
| 2ZXN A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket Deposited 2009-01-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-423
|
Not recorded | JC1 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2S,3S)-3-(2-hydroxyethyl)heptan-2-yl]-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 7；293 K；MOPS-Na, Na-Formate, PEG4000, Ethyleneglycol, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.251 |
| 3A2H Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2009-05-20 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：ligand binding domain, residues 116-423
Chain A
212–423（212 aa）
Fragment：ligand binding domain, residues 116-423
|
Mutation：DEL(165-211) mutant Mutation：DEL(165-211) 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 7；293 K；1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.309 |
| 3A2H Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2009-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–164（49 aa）
Fragment：ligand binding domain, residues 116-423
Chain A
212–423（212 aa）
Fragment：ligand binding domain, residues 116-423
|
Mutation：DEL(165-211) mutant Mutation：DEL(165-211) 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 7；293 K；1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.50 Å R-free 0.309 |
| 3AFR Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex Deposited 2010-03-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, residues 116-423
|
Mutation：deletion mutant, residues 165-211 | ICJ (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.264 |
| 3AUN Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205 Deposited 2011-02-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：ligand binding domain
Chain A
212–423（212 aa）
Fragment：ligand binding domain
|
Mutation：DEL(165-211) mutant Mutation：DEL(165-211) mutant | YR4 (2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.81 Å R-free 0.237 |
| 3VJS Vitamin D receptor complex with a carborane compound Deposited 2011-10-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand-binding domain, UNP residues 116-423
|
Mutation：deletion of UNP residues 165-211 | 10S 1-(2-[(S)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS/NaOH, 0.1-0.4M sodium formate, 12-22% PEG 4000, 5% ethylene glycol
, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.93 Å R-free 0.282 |
| 3VJT Vitamin D receptor complex with a carborane compound Deposited 2011-10-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：ligand-binding domain, UNP residues 116-423
|
Mutation：deletion of UNP residues 165-211 | 10R 1-(2-[(R)-2,4-Dihydroxybutoxy]ethyl)-12-(5-ethyl-5-hydroxyheptyl)-1,12-dicarba-closo-dodecaborane × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS/NaOH, 0.1-0.4M sodium formate, 12-22% PEG 4000, 5% ethylene glycol
, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.266 |
| 3VRT VDR ligand binding domain in complex with 2-Mehylidene-19,25,26,27-tetranor-1alpha,24-dihydroxyvitaminD3 Deposited 2012-04-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, residues 116-423
|
Mutation：deletion mutant, residues 165-211 | YS2 (1R,3R,7E,17beta)-17-[(2R)-5-hydroxypentan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.40 Å R-free 0.273 |
| 3VRU VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3 Deposited 2012-04-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, residues 116-423
|
Mutation：deletion mutant, residues 165-211 | YS3 (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MES-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.00 Å R-free 0.279 |
| 3VRV VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 Deposited 2012-04-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, residues 116-423
|
Mutation：deletion mutant, residues 165-211 | YSD (1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MES-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.90 Å R-free 0.248 |
| 3VRW VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 Deposited 2012-04-16 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, residues 116-423
|
Mutation：deletion mutant, residues 165-211 | YS5 (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MES-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 2.40 Å R-free 0.256 |
| 3VT3 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris-HCl, sodium formate, PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.241 |
| 3VT3 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Tris-HCl, sodium formate, PEG 4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.70 Å R-free 0.241 |
| 3VT4 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | 5YI (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.260 |
| 3VT4 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | 5YI (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.260 |
| 3VT5 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | YI2 (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.11 Å R-free 0.266 |
| 3VT5 Crystal structures of rat VDR-LBD with R270L mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：R270L | YI2 (1R,2E,3R,5Z,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.11 Å R-free 0.266 |
| 3VT6 Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Not recorded | 5YI (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.245 |
| 3VT6 Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Not recorded | 5YI (1R,2Z,3R,5E,7E)-17-{(1S)-1-[(2-ethyl-2-hydroxybutyl)sulfanyl]ethyl}-2-(2-hydroxyethylidene)-9,10-secoestra-5,7,16-triene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.245 |
| 3VT7 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.65 Å R-free 0.229 |
| 3VT7 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | VDX 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.65 Å R-free 0.229 |
| 3VT8 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | YI3 (1R,3R,7E,9beta,17beta)-9-butyl-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, HANGING DROP；pH 7；293 K；MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.235 |
| 3VT8 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | YI3 (1R,3R,7E,9beta,17beta)-9-butyl-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, HANGING DROP；pH 7；293 K；MOPS-Na, di-Ammonium Citrate, PEG 4000, 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.235 |
| 3VT9 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | YI4 (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.250 |
| 3VT9 Crystal structures of rat VDR-LBD with W282R mutation Deposited 2012-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Mutation：W282R | YI4 (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, sodium formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.35 Å R-free 0.250 |
| 3VTB Crystal structure of rat vitamin D receptor bound to a partial agonist 25-adamantyl-23-yne-19-norvitammin D ADTK1 Deposited 2012-05-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Not recorded | TKA (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-6-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hex-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.286 |
| 3VTC Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK3 Deposited 2012-05-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Not recorded | TK3 (1R,3R,7E,17beta)-17-{(2R,6R)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.50 Å R-free 0.209 |
| 3VTD Crystal structure of rat vitamin D receptor bound to a partial agonist 26-adamantyl-23-yne-19-norvitammin D ADTK4 Deposited 2012-05-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-423
|
Not recorded | TKD (1R,3R,7E,17beta)-17-{(2R,6S)-6-hydroxy-7-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]hept-4-yn-2-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na formate, PEG 4000, ethyleneglycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.70 Å R-free 0.278 |
| 3W0G Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands Deposited 2012-10-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–420（300 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 121-164, 212-420
|
Not recorded | W07 (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)propan-2-yl]phenoxy}propane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS(pH7.0), 16-18% PEG4000, 0.2M sodium formate, 5% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.94 Å R-free 0.258 |
| 3W0H Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands Deposited 2012-10-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
118–420（303 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 116-164, 212-420
|
Not recorded | W12 (2S)-3-{4-[4-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)heptan-4-yl]phenoxy}propane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS (pH7.0), 16-18% PEG 4000, 0.2M sodium formate, 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.80 Å R-free 0.230 |
| 3W0I Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands Deposited 2012-10-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–420（300 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 121-159, 218-420
|
Not recorded | O11 (2S)-3-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}phenyl)pentan-3-yl]phenoxy}propane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS (pH7.0), 16-18% PEG 4000, 0.2M sodium formate, 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.90 Å R-free 0.279 |
| 3W0J Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel Nonsecosteroidal Ligands Deposited 2012-10-30 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
121–420（300 aa）
Fragment：LIGAND BINDING DOMAIN, UNP residues 121-164, 212-420
|
Not recorded | T08 (2S)-3-{4-[2-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)propan-2-yl]-2-methylphenoxy}propane-1,2-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS (pH7.0), 16-18% PEG 4000, 0.2M sodium formate, 5% ethylene glycol , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.84 Å R-free 0.259 |
| 3W5P Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives Deposited 2013-02-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP RESIDUES 116-423
|
Not recorded | 4OA (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.5 K；0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4 M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
|
Resolution 1.90 Å R-free 0.263 |
| 3W5Q Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives Deposited 2013-02-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP RESIDUES 116-423
|
Not recorded | 3KL (5beta,9beta)-3-oxocholan-24-oic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.5 K；0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
|
Resolution 1.90 Å R-free 0.279 |
| 3W5R Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives Deposited 2013-02-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP RESIDUES 116-423
|
Not recorded | LOA (3beta,5beta,9beta)-3-(acetyloxy)cholan-24-oic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.5 K；0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
|
Resolution 2.20 Å R-free 0.276 |
| 3W5T Crystal structure of complexes of vitamin D receptor ligand binding domain with lithocholic acid derivatives Deposited 2013-02-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：VDR-LBD, UNP RESIDUES 116-423
|
Not recorded | LHP (3beta,5beta,9beta)-3-(propanoyloxy)cholan-24-oic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.5 K；0.1M 3-(N-morpholino) propanesulfonic acid/sodium hydroxide, 0.1-0.4M sodium formate, 12-22% PEG 4000, 0-10% ethylene glycol , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
|
Resolution 2.29 Å R-free 0.265 |
| 3WT5 A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group Deposited 2014-04-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-164, 212-423
|
Not recorded | YA1 (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.189 |
| 3WT6 A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group Deposited 2014-04-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-164, 212-423
|
Not recorded | YA1 (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.224 |
| 3WT7 Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3 Deposited 2014-04-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-164, 212-423
|
Not recorded | YA2 (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.40 Å R-free 0.194 |
| 3WTQ Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 Deposited 2014-04-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：Ligand binding domain, UNP residues 116-423
|
Not recorded | YS9 (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.275 |
| 4YNK Crystal structure of vitamin D receptor ligand binding domain complexed with a 19-norvitamin D compound Deposited 2015-03-10 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：UNP residues 116-164,212-423,UNP residues 116-164,212-423
Chain A
212–423（212 aa）
Fragment：UNP residues 116-164,212-423,UNP residues 116-164,212-423
|
Not recorded | YW2 (1R,3R,7E,17beta)-17-{(5S)-5-hydroxy-5-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-1-yl]penta-1,3-diyn-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；MOPS, Sodium Formate, PEG4000, Ethylene glycol
|
Resolution 2.30 Å R-free 0.257 |
| 5AWJ Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue Deposited 2015-07-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：UNP RESIDUES 116-164, 212-423
Chain A
212–423（212 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
Not recorded | YSL (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.20 Å R-free 0.260 |
| 5AWK Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue Deposited 2015-07-04 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–164（49 aa）
Fragment：UNP RESIDUES 116-164, 212-423
Chain A
212–423（212 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
Not recorded | YSE (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.90 Å R-free 0.267 |
| 5B41 Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 Deposited 2016-03-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
Mutation：165-211 deletion | YSV (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-formate, PEG 4000, Ethyleneglycol
|
Resolution 1.89 Å R-free 0.234 |
| 5B5B Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3 Deposited 2016-05-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
Mutation：165-211 deletion | AKX (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.00 Å R-free 0.230 |
| 5B5B Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3 Deposited 2016-05-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
116–423（308 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
Mutation：165-211 deletion | AKX (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.00 Å R-free 0.230 |
| 5GIC Crystal structure of VDR in complex with DLAM-2P Deposited 2016-06-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
124–164（41 aa）
Fragment：UNP RESIDUES 124-164,UNP RESIDUES 212-420
Chain A
212–420（209 aa）
Fragment：UNP RESIDUES 124-164,UNP RESIDUES 212-420
|
Not recorded | DLC (3~{R},5~{S})-5-[(2~{R})-2-[(1~{R},3~{a}~{S},4~{Z},7~{a}~{R})-7~{a}-methyl-4-[(2~{E})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(2-phenylethyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Tris-HCl, PEG 8000,
NaCl
|
Resolution 2.35 Å R-free 0.251 |
| 5GID Crystal structure of VDR in complex with DLAM-4 (C2 form) Deposited 2016-06-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
124–164（41 aa）
Fragment：UNP RESIDUES 124-164,UNP RESIDUES 212-419
Chain A
212–419（208 aa）
Fragment：UNP RESIDUES 124-164,UNP RESIDUES 212-419
|
Not recorded | VDP (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Tris-HCl, PEG 8000, NaCl
|
Resolution 2.15 Å R-free 0.233 |
| 5GIE Crystal structure of VDR in complex with DLAM-4P (P21 form) Deposited 2016-06-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
117–164（48 aa）
Fragment：UNP RESIDUES 117-164,UNP RESIDUES 212-419
Chain A
212–419（208 aa）
Fragment：UNP RESIDUES 117-164,UNP RESIDUES 212-419
|
Not recorded | VDP (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Tris-HCl, PEG 8000, NaCl
|
Resolution 2.39 Å R-free 0.234 |
| 5GIE Crystal structure of VDR in complex with DLAM-4P (P21 form) Deposited 2016-06-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
117–164（48 aa）
Fragment：UNP RESIDUES 117-164,UNP RESIDUES 212-419
Chain D
212–419（208 aa）
Fragment：UNP RESIDUES 117-164,UNP RESIDUES 212-419
|
Not recorded | VDP (3R,5S)-5-[(2R)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[(2Z)-2-[(3S,5R)-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]propyl]-3-methyl-3-oxidanyl-1-(4-phenylbutyl)pyrrolidin-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Tris-HCl, PEG 8000, NaCl
|
Resolution 2.39 Å R-free 0.234 |
| 5H1E Interaction between vitamin D receptor and coactivator peptide SRC2-3 Deposited 2016-10-08 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP RESIDUES 116-164, 212-423
|
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；293 K；MOP-Na, Na-Formate, PEG 4000, Ethleneglycol
|
Resolution 2.60 Å R-free 0.248 |
| 5XPL Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 Deposited 2017-06-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion mutant(residues 165-211) | 8C9 (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl )cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethylenglycol
|
Resolution 2.05 Å R-free 0.242 |
| 5XPM Crystal structure of VDR-LBD complexed with 22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 Deposited 2017-06-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion mutant(residues 165-211) | 8C0 (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.20 Å R-free 0.248 |
| 5XPN Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3 Deposited 2017-06-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion mutant(residues 165-211) | 8BO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 9RO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 1.96 Å R-free 0.256 |
| 5XPO Crystal structure of VDR-LBD complexed with 25-(hydroxyphenyl)-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3 Deposited 2017-06-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion mutant(residues 165-211) | 8BL (5~{R})-5-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexyl idene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-(4-hydroxyphenyl)hexan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.28 Å R-free 0.275 |
| 5XPP Crystal structure of VDR-LBD complexed with 25RS-(Hydroxyphenyl)-2-methylidene-19,26,27-trinor-1,25-dihydroxyvitamin D3 Deposited 2017-06-03 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion mutant(residues 165-211) | 8BF (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.85 Å R-free 0.250 |
| 5XUQ Crystal structure of VDR-LBD complexed with an antagonist, 2-methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H-pyrrol-2-yl)- vitamin D3 Deposited 2017-06-24 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：deletion 165-211 | 8FF (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.80 Å R-free 0.196 |
| 5XZF Vitamin D receptor with a synthetic ligand ADRO1 Deposited 2017-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：165-211 deletion | 8J0 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6S)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MOPS/NaOH, 0.2M sodium formate, 14-18%(w/v) PEG4000, 8%(v/v) ethylene glycol
|
Resolution 2.10 Å R-free 0.214 |
| 5XZH Vitamin D receptor with a synthetic ligand ADRO2 Deposited 2017-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
Fragment：UNP residues 116-423
|
Mutation：165-211 deletion | 8J3 (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6R)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-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；293 K；0.1M MOPS/NaOH, 0.2M sodium formate, 14-18%(w/v) PEG4000, 8% (v/v) ethylene glycol
|
Resolution 2.00 Å R-free 0.243 |
| 5ZWE Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a vinyl ketone group via conjugate addition reaction Deposited 2018-05-15 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Mutation：165-211 deletion | 9K0 (6R)-6-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]hept-1-en-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.72 Å R-free 0.252 |
| 5ZWF Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having a enone with a beta methyl group via conjugate addition reaction Deposited 2018-05-15 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Mutation：165-211 deletion | 9KR (E,7R)-7-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-2-en-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.10 Å R-free 0.250 |
| 5ZWH Covalent bond formation between histidine of Vitamin D receptor (VDR) and a full agonist having an ene-ynone group via conjugate addition reaction Deposited 2018-05-15 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Mutation：165-211 deletion | 9KX (2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-4,6-diene-3-one × 1 9N9 (E,2S)-2-[(1R,3aS,4E,7aR)-7a-methyl-4-[2-[(3R,5R)-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3a,5,6,7-hexahydro-1H-inden-1-yl]oct-6-en-4-yn-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；MOPS-Na, Na-Formate, PEG 4000, Ethyleneglycol
|
Resolution 2.38 Å R-free 0.279 |
| 6JEZ Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition and cyclization Deposited 2019-02-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–163（48 aa）
Chain A
213–423（211 aa）
|
Not recorded | YSV (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol × 1 EJO 7-(diethylamino)chromen-2-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MOPS-Na pH 7.0, 0.1 M sodium formate, 15% PEG4000, 5% ethylene glycol
|
Resolution 2.30 Å R-free 0.256 |
| 6K5O Development of Novel Lithocholic Acid Derivatives as Vitamin D Receptor Agonists Deposited 2019-05-29 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–419（304 aa）
|
Mutation：165-211 deletion | D0O (4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3-methylsulfonyloxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M MOPS/NaOH (pH 7.0), 0.1-0.4 M sodium formate, 12-22% (w/v) PEG4000, and 5%
(v/v) ethylene glycol
|
Resolution 1.80 Å R-free 0.257 |
| 7C7V Vitamin D3 receptor/lithochoric acid derivative complex Deposited 2020-05-26 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Mutation：deletion 166-212 | FKC (4R)-4-[(3R,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol
|
Resolution 2.00 Å R-free 0.268 |
| 7C7W Vitamin D3 receptor/lithochoric acid derivative complex Deposited 2020-05-26 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Mutation：deletion 166-212 | FKF (4R)-4-[(3S,5R,8R,9S,10S,13R,14S,17R)-10,13-dimethyl-3-(2-methyl-2-oxidanyl-propyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-17-yl]pentanoic acid × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M MOPS-NaOH (pH 7.0), 0.2 M sodium formate, 12% (w/v) PEG4000, and 8% (v/v) ethylene glycol
|
Resolution 1.90 Å R-free 0.248 |
| 9M10 Vitamin D receptor complex with a dimethylbis((3-trifluoromethyl)phenyl)silane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L7X (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-(trifluoromethyl)phenyl]-dimethyl-silyl]-2-(trifluoromethyl)phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium acetate tetrahydrate, PEG 3350, pH 7.9.
|
Resolution 2.02 Å R-free 0.222 |
| 9M11 Vitamin D receptor complex with a bis(3-chlorophenyl)dimethylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L7Y (4~{S})-5-[2-chloranyl-4-[[3-chloranyl-4-(2-ethyl-2-oxidanyl-butoxy)phenyl]-dimethyl-silyl]phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, sodium formate, pH 7.2
|
Resolution 2.05 Å R-free 0.243 |
| 9M12 Vitamin D receptor complex with a bis(3-ethylphenyl)dimethylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L7Z (4~{S})-5-[2-ethyl-4-[[3-ethyl-4-(2-ethyl-2-oxidanyl-butoxy)phenyl]-dimethyl-silyl]phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, magnesium formate dihydrate, pH 7.
|
Resolution 1.86 Å R-free 0.217 |
| 9M12 Vitamin D receptor complex with a bis(3-ethylphenyl)dimethylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
116–423（308 aa）
|
Not recorded | A1L7Z (4~{S})-5-[2-ethyl-4-[[3-ethyl-4-(2-ethyl-2-oxidanyl-butoxy)phenyl]-dimethyl-silyl]phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, magnesium formate dihydrate, pH 7.
|
Resolution 1.86 Å R-free 0.217 |
| 9M13 Vitamin D receptor complex with a dimethyldiphenylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L70 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)phenyl]-dimethyl-silyl]phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Sodium malonate, pH 6.
|
Resolution 1.68 Å R-free 0.198 |
| 9M14 Vitamin D receptor complex with a dimethyldi(m-tolyl)silane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L71 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-dimethyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, magnesium formate dihydrate, pH 7.
|
Resolution 2.00 Å R-free 0.232 |
| 9M15 Vitamin D receptor complex with a dimethyldi(o-tolyl)silane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L73 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-2-methyl-phenyl]-dimethyl-silyl]-3-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Magnesium acetate tetrahydrate, pH 7.9
|
Resolution 2.18 Å R-free 0.229 |
| 9M16 Vitamin D receptor complex with a bis(2,3-dimethylphenyl)dimethylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L74 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-2,3-dimethyl-phenyl]-dimethyl-silyl]-2,3-dimethyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Lithium citrate tribasic tetrahydrate, pH 8.4
|
Resolution 2.06 Å R-free 0.195 |
| 9M17 Vitamin D receptor complex with a bis(3,5-dimethylphenyl)dimethylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L75 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3,5-dimethyl-phenyl]-dimethyl-silyl]-2,6-dimethyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Sodium citrate tribasic dihydrate, pH 8.3
|
Resolution 1.81 Å R-free 0.213 |
| 9M18 Vitamin D receptor complex with a diallyldiphenylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L76 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-bis(prop-2-enyl)silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Sodium phosphate dibasic dihydrate, pH 9.1
|
Resolution 1.96 Å R-free 0.236 |
| 9M19 Vitamin D receptor complex with a dibutyldiphenylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L77 (4~{S})-5-[4-[dibutyl-[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Tacsimate pH 7.0, HEPES pH 7.5
|
Resolution 2.05 Å R-free 0.230 |
| 9M1A Vitamin D receptor complex with a diethyldiphenylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L78 (4~{S})-5-[4-[diethyl-[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Tacsimate, pH 7.0
|
Resolution 1.78 Å R-free 0.211 |
| 9M1B Vitamin D receptor complex with a diphenydipropylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L79 (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-dipropyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Cesium chloride
|
Resolution 1.77 Å R-free 0.213 |
| 9M1C Vitamin D receptor complex with a triphenylpropylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L8A (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-phenyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, DL-Malic acid, pH 7.0
|
Resolution 1.67 Å R-free 0.201 |
| 9M1D Vitamin D receptor complex with a methyldiphenylpropylsilane derivative Deposited 2025-02-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1L8B (4~{S})-5-[4-[[4-(2-ethyl-2-oxidanyl-butoxy)-3-methyl-phenyl]-methyl-propyl-silyl]-2-methyl-phenoxy]-4-oxidanyl-pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Lithium citrate tribasic tetrahydrate, pH 8.4
|
Resolution 1.44 Å R-free 0.210 |
| 9VOG Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAV (S)-5-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]-4-hydroxypentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium citrate tribasic monohydrate pH 8.3, 20% w/v PEG 3350
|
Resolution 1.43 Å R-free 0.220 |
| 9VOH Vitamin D receptor complex with a 4-(m-carboran-1-yl)phenoxyacetic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAW [4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba- closo-dodecaboran-1-yl}phenoxy]acetic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Ammonium Citrate Tribasic pH 7.0, 20% w/v PEG 3350
|
Resolution 1.98 Å R-free 0.225 |
| 9VOI Vitamin D receptor complex with a 3-{4-(m-carboran-1-yl)phenoxy}propanoic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAX 3-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]propionic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.03M citric acid, 0.07M BIS-TRIS propane pH 7.6, 20% w/v PEG 3350
|
Resolution 1.93 Å R-free 0.201 |
| 9VOJ Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)phenoxy}butanoic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAY 4-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]butyric acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.01M MagnesiumChloride hexahydrate, 0.005M Nickle(II) chloride hexahydrate, 0.1m HEPES solution pH 7.0, 15% w/v PEG 3350
|
Resolution 1.93 Å R-free 0.216 |
| 9VOK Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}pentanoic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAZ 5-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}phenoxy]pentanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M DL-Malic acid pH 7.0, 12% w/v PEG 3350
|
Resolution 2.04 Å R-free 0.273 |
| 9VOL Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid derivative Deposited 2025-07-01 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
116–423（308 aa）
|
Not recorded | A1MAU 4-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba-closo-dodecaboran-1-yl}-2-methylphenoxy]butyric acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2M Sodium malonate pH 7.0, 8% v/v Tacsimate pH 7.0, 20% w/v PEG 3350
|
Resolution 1.75 Å R-free 0.210 |
90 other PDB entries and 109 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | VDR_RAT |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 11–271； UniProt 116–423 |
