Research workbench
Crystal structure of the ligand-binding domains of the heterodimer ECR/USP bound to the synthetic agonist BYI06830
Analyse Crystal structure of the ligand-binding domains of the heterodimer ECR/USP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R20
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ultraspiracle protein; Ecdysone receptor
- UniProt
- Q7SIF6, O18473
- Ligands
- EPH, HWG
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ultraspiracle protein | protein | 239 | 64% helix, 5% strand | Q7SIF6 |
| D | Ecdysone receptor | protein | 228 | 64% helix, 2% strand | O18473 |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains A
- HWG · N-(tert-butyl)-3,5-dimethyl-N'-[(5-methyl-2,3-dihydro-1,4-benzodioxin-6-yl)carbonyl]benzohydrazide · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.83 | 0.88 | 34 | EPH |
| 2 | 245 | 0.81 | 0.92 | 25 | HWG |
| 3 | 497 | 0.72 | 0.81 | 46 | empty |
| 4 | 219 | 0.65 | 0.84 | 42 | empty |
| 5 | 262 | 0.57 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–D · 1260 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1R20 · Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the… · the same entry in another collection · chain A against A, TM-score 1.00
- O18473 · AlphaFold monomer V2.0 prediction for ecdysone receptor (O18473) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q7SIF6
- Every structure of UniProt O18473
- Elsewhere: RCSB PDB 1R20 · PDBe 1R20 · UniProt Q7SIF6 · UniProt O18473
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