Research workbench
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
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
- 5YT2
- Type
- protein
- Length
- 255 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor
- UniProt
- P11473
- Ligands
- 90O
- 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 | 255 | 66% helix, 3% strand | P11473 |
Ligands and binding sites
- 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 · 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 | 317 | 0.86 | 0.95 | 37 | 90O |
Compared structures
- 5YT2 · 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
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 5YT2 · PDBe 5YT2 · UniProt P11473
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