MolNFT v1 · #184664 · protein
Vdr complex of a side-chain hydroxylated derivatives of lithocholic acid
7OY4 · Vitamin D3 receptor a: “Vdr complex of a side-chain hydroxylated derivatives of lithocholic acid”. X-ray diffraction, 1 ligand (2WV), 3 pockets (best druggability 0.86). MolNFT v1 #184664 on GenesisL1: 3D structure, binding sites…
- PDB
- 7OY4
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor a; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q9PTN2, Q15788
- Ligands
- 2WV
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor a | protein | 238 | 68% helix, 3% strand | Q9PTN2 |
| B | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 10 | 60% helix, 0% strand | Q15788 |
Ligands and binding sites
- 2WV · (3S,6R)-6-[(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]heptane-1,3-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.86 | 0.95 | 37 | 2WV |
| 2 | 208 | 0.51 | 0.77 | 30 | empty |
| 3 | 59 | 0.32 | 0.77 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 617 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7OY4 · VDR complex of a side-chain hydroxylated derivatives of lithocholic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9PTN2
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 7OY4 · PDBe 7OY4 · UniProt Q9PTN2 · UniProt Q15788
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