Research workbench
X-ray structure of benzisoxazole synthetic agonist bound to the lxr- alpha
Analyse X-ray structure of benzisoxazole synthetic agonist bound to the lxr- alpha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IPS
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-alpha; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- Q13133, Q15788
- Ligands
- O90, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-alpha | protein | 224 | 68% helix, 3% strand | Q13133 |
| B | Oxysterols receptor lxr-alpha | protein | 226 | 68% helix, 4% strand | Q13133 |
| C, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 15 | 80% helix, 0% strand | Q15788 |
Ligands and binding sites
- O90 · {3-chloro-4-[(3-{[7-propyl-3-(trifluoromethyl)-1,2-benzisoxazol-6-yl]oxy}propyl)sulfanyl]phenyl}acetic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.81 | 0.91 | 32 | O90 |
| 2 | 274 | 0.80 | 0.91 | 29 | O90 |
| 3 | 665 | 0.74 | 0.80 | 57 | empty |
| 4 | 600 | 0.73 | 0.80 | 60 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1202 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 729 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 718 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3IPS · X-ray structure of benzisoxazole synthetic agonist bound to the LXR-alpha · the same entry in another collection · chain B against B, TM-score 1.00
- Q13133 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-alpha (Q13133) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q13133
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 3IPS · PDBe 3IPS · UniProt Q13133 · UniProt Q15788
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