Research workbench
Human LXR-beta in complex with an agonist
Analyse Human LXR-beta in complex with an agonist in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K9H
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Homo sapiens
- Molecule
- Oxysterols receptor LXR-beta
- UniProt
- P55055
- Ligands
- D40
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.5 · 2 distinct chains · 70% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor LXR-beta | protein | 227 | 70% helix, 3% strand | P55055 |
| B | Oxysterols receptor LXR-beta | protein | 227 | 71% helix, 1% strand | P55055 |
Ligands and binding sites
- D40 · ~{tert}-butyl (2'~{S},3~{S})-2-oxidanylidene-2'-phenyl-spiro[1~{H}-indole-3,3'-pyrrolidine]-1'-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 438 | 0.83 | 0.90 | 50 | D40 |
| 2 | 623 | 0.81 | 0.85 | 49 | D40 |
| 3 | 637 | 0.75 | 0.81 | 69 | empty |
| 4 | 309 | 0.65 | 0.80 | 39 | empty |
| 5 | 105 | 0.50 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 953 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 P55055
- Elsewhere: RCSB PDB 6K9H · PDBe 6K9H · UniProt P55055
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