MolNFT v1 · #17926 · protein
X-ray crystal structure of lxr ligand binding domain with 24(S),25- epoxycholesterol
1P8D · Oxysterols receptor lxr-beta: “X-ray crystal structure of lxr ligand binding domain with 24(S),25- epoxycholesterol”. X-ray diffraction, 1 ligand (CO1), 4 pockets (best druggability 0.86). MolNFT v1 #17926 on GenesisL1: 3D…
- PDB
- 1P8D
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterols receptor lxr-beta; Nuclear receptor coactivator 1 isoform 3
- UniProt
- P55055
- Ligands
- CO1
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterols receptor lxr-beta | protein | 240 | 65% helix, 3% strand | P55055 |
| B | Oxysterols receptor lxr-beta | protein | 239 | 67% helix, 2% strand | P55055 |
| C | Nuclear receptor coactivator 1 isoform 3 | protein | 16 | 50% helix, 0% strand | — |
| D | Nuclear receptor coactivator 1 isoform 3 | protein | 13 | 69% helix, 0% strand | — |
Ligands and binding sites
- CO1 · 17-[3-(3,3-dimethyl-oxiranyl)-1-methyl-propyl]-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-ol · ligand · 2 copies · chains A, B
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 | 349 | 0.86 | 0.94 | 43 | CO1 |
| 2 | 354 | 0.85 | 0.94 | 39 | CO1 |
| 3 | 1140 | 0.81 | 0.82 | 103 | empty |
| 4 | 117 | 0.60 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1124 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 616 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1P8D · X-Ray Crystal Structure of LXR Ligand Binding Domain with 24(S),25-epoxycholesterol · the same entry in another collection · chain A against A, TM-score 1.00
- P55055 · AlphaFold monomer V2.0 prediction for oxysterols receptor lxr-beta (P55055) · a predicted model of the same protein · chain B 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
- Elsewhere: RCSB PDB 1P8D · PDBe 1P8D · UniProt P55055
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