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Crystal structure of the ligand-binding domains of the heterodimer ECR/USP bound to the synthetic agonist BYI09181
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
- 7BJV
- Type
- protein
- Length
- 1,441 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ultraspiracle protein; Ecdysone receptor
- UniProt
- A0A2A4K9Z3
- Ligands
- EPH, U0H, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ultraspiracle protein | protein | 249 | 61% helix, 5% strand | A0A2A4K9Z3 |
| B | Ultraspiracle protein | protein | 247 | 61% helix, 5% strand | A0A2A4K9Z3 |
| C | Ultraspiracle protein | protein | 252 | 60% helix, 5% strand | A0A2A4K9Z3 |
| D | Ecdysone receptor | protein | 240 | 66% helix, 2% strand | — |
| E | Ecdysone receptor | protein | 223 | 67% helix, 2% strand | — |
| F | Ecdysone receptor | protein | 230 | 65% helix, 2% strand | — |
Ligands and binding sites
- EPH · L-alpha-phosphatidyl-beta-oleoyl-gamma-palmitoyl-phosphatidylethanolamine · ligand · 3 copies · chains A, B, C
- U0H · ~{N}-~{tert}-butyl-2-methoxy-~{N}'-(3-methoxy-2-methyl-phenyl)carbonyl-pyridine-3-carbohydrazide · ligand · 3 copies · chains D, E, F
- MG · Magnesium ion · metal · chains D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.84 | 0.86 | 68 | U0H |
| 2 | 505 | 0.83 | 0.89 | 33 | EPH |
| 3 | 712 | 0.83 | 0.86 | 59 | EPH |
| 4 | 188 | 0.82 | 0.96 | 23 | U0H |
| 5 | 850 | 0.82 | 0.84 | 74 | U0H |
Interfaces
10 interfaces between chains.
- B–E · 1363 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1321 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1297 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 569 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7BJV · 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 7BJV · PDBe 7BJV · UniProt A0A2A4K9Z3
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