MolNFT v1 · #38876 · protein
Crystal structure of the lbd of vdr of danio rerio in complex with calcitriol
2HC4 · Vitamin D receptor: “Crystal structure of the lbd of vdr of danio rerio in complex with calcitriol”. X-ray diffraction, 1 ligand (VDX), 2 pockets (best druggability 0.86). MolNFT v1 #38876 on GenesisL1: 3D structure, binding sites…
- PDB
- 2HC4
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D receptor; Src-1 from nuclear receptor coactivator 1
- UniProt
- Q9PTN2, Q15788
- Ligands
- VDX
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D receptor | protein | 239 | 64% helix, 3% strand | Q9PTN2 |
| B | Src-1 from nuclear receptor coactivator 1 | protein | 10 | 60% helix, 0% strand | Q15788 |
Ligands and binding sites
- VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-1,3-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.86 | 0.96 | 36 | VDX |
| 2 | 162 | 0.44 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 567 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2HC4 · Crystal structure of the LBD of VDR of Danio rerio in complex with calcitriol · 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 0.97
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 2HC4 · PDBe 2HC4 · UniProt Q9PTN2 · UniProt Q15788
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