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Crystal structure of the ligand-binding domains of the heterodimer EcR/USP bound to the synthetic agonist BYI08346
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
- 7BJU
- Type
- protein
- Length
- 479 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- Heliothis virescens
- Molecule
- Ultraspiracle Protein; Ecdysone Receptor
- UniProt
- A0A2A4K9Z3
- Ligands
- EPH, 834, MG
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.85 · 2 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ultraspiracle Protein | protein | 248 | 61% helix, 5% strand | A0A2A4K9Z3 |
| D | Ecdysone Receptor | protein | 231 | 68% helix, 2% strand | — |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · chains A
- 834 · N-[2-(2-chlorophenyl)-4-methyl-5-(1-methylethyl)-1H-imidazol-1-yl]-5-methyl-2,3-dihydro-1,4-benzodioxine-6-carboxamide · ligand · chains D
- MG · Magnesium ion · metal · chains D
- PEG · Di(hydroxyethyl)ether · additive · chains A, D
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · chains D
- PGE · Triethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.83 | 0.89 | 35 | EPH |
| 2 | 189 | 0.82 | 0.95 | 25 | 834 |
| 3 | 414 | 0.70 | 0.81 | 46 | empty |
| 4 | 324 | 0.63 | 0.79 | 26 | empty |
| 5 | 192 | 0.59 | 0.81 | 32 | empty |
Interfaces
1 interface between chains.
- A–D · 1332 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7BJU · 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
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 A0A2A4K9Z3
- Elsewhere: RCSB PDB 7BJU · PDBe 7BJU · UniProt A0A2A4K9Z3
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