Research workbench
Crystal structure of rat vitamin D receptor ligand binding domain complexed with vitiii 17-20Z and the NR2 box of drip 205
Analyse Crystal structure of rat vitamin D receptor ligand binding domain complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O4J
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Peroxisome proliferator-activated receptor-binding protein
- UniProt
- P13053, Q15648
- Ligands
- VD4
- Pockets
- 2 · 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 | protein | 240 | 69% helix, 3% strand | P13053 |
| C | Peroxisome proliferator-activated receptor-binding protein | protein | 12 | 58% helix, 0% strand | Q15648 |
Ligands and binding sites
- VD4 · (1R,3R,7E,17Z)-17-(5-hydroxy-1,5-dimethylhexylidene)-2-methylene-9,10-secoestra-5,7-diene-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 | 286 | 0.86 | 0.96 | 35 | VD4 |
| 2 | 84 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–C · 541 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2O4J · Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII… · the same entry in another collection · chain A against A, TM-score 1.00
- P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.62
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 P13053
- Every structure of UniProt Q15648
- Elsewhere: RCSB PDB 2O4J · PDBe 2O4J · UniProt P13053 · UniProt Q15648
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.