MolNFT v1 · #89264 · protein
Crystal structure of lxr ligand binding domain in complex with full agonist 1
4DK7 · Oxysterols receptor lxr-beta: “Crystal structure of lxr ligand binding domain in complex with full agonist 1”. X-ray diffraction, 2 ligands (0KS, CA), 5 pockets (best druggability 0.83). MolNFT v1 #89264 on GenesisL1: 3D structure…
- PDB
- 4DK7
- Type
- protein
- Length
- 488 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-beta; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P55055, Q15788
- Ligands
- 0KS, CA
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-beta | protein | 235 | 69% helix, 3% strand | P55055 |
| B, D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 12 | 67% helix, 0% strand | Q15788 |
| C | Oxysterols receptor lxr-beta | protein | 229 | 69% helix, 3% strand | P55055 |
Ligands and binding sites
- 0KS · N-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-N-methylbenzenesulfonamide · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 7 copies · chains A, C
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.83 | 0.95 | 29 | 0KS |
| 2 | 1071 | 0.81 | 0.82 | 104 | empty |
| 3 | 323 | 0.77 | 0.88 | 39 | 0KS |
| 4 | 80 | 0.50 | 0.84 | 22 | empty |
| 5 | 52 | 0.34 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1117 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 722 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 602 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (engineered).
Compared structures
- 4DK7 · Crystal structure of LXR ligand binding domain in complex with full agonist 1 · the same entry in another collection · chain D against D, TM-score 1.00
- P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain C 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 P55055
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 4DK7 · PDBe 4DK7 · UniProt P55055 · UniProt Q15788
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