Research workbench
Crystal structure of the lbd of vdr of danio rerio in complex with calcitriol
Analyse Crystal structure of the lbd of vdr of danio rerio in complex with calcitriol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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