Research workbench
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
Analyse Crystal structure of the human vitamin D receptor ligand binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WWR
- Type
- protein
- Length
- 254 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor
- UniProt
- P11473
- Ligands
- 3AJ
- Pockets
- 1 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 254 | 66% helix, 3% strand | P11473 |
Ligands and binding sites
- 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 · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.86 | 0.94 | 39 | 3AJ |
Compared structures
- 3WWR · Crystal structure of the human vitamin D receptor ligand binding domain complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P11473
- Elsewhere: RCSB PDB 3WWR · PDBe 3WWR · UniProt P11473
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