Research workbench
Structure of pregnane X receptor in complex with a sphingosine 1- phosphate receptor 1 antagonist
Analyse Structure of pregnane X receptor in complex with a sphingosine 1- phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A86
- Type
- protein
- Length
- 577 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- O75469, Q15788
- Ligands
- D7E
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2 | protein | 271 | 60% helix, 7% strand | O75469 |
| B | Nuclear receptor subfamily 1 group I member 2 | protein | 274 | 61% helix, 8% strand | O75469 |
| C | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 15 | 47% helix, 0% strand | Q15788 |
| D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 17 | 76% helix, 0% strand | Q15788 |
Ligands and binding sites
- D7E · 4-chloro-N-[(1R)-1-[1-ethyl-6-(trifluoromethyl)benzimidazol-2-yl]ethyl]benzenesulfonamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.86 | 0.94 | 38 | D7E |
| 2 | 477 | 0.85 | 0.91 | 50 | D7E |
| 3 | 91 | 0.37 | 0.76 | 17 | empty |
| 4 | 54 | 0.37 | 0.79 | 14 | empty |
| 5 | 53 | 0.32 | 0.77 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 783 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 653 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 611 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5A86 · Structure of pregnane X receptor in complex with a Sphingosine 1- Phosphate Receptor 1… · the same entry in another collection · chain A against A, TM-score 1.00
- O75469 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 1 group I member 2… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O75469
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 5A86 · PDBe 5A86 · UniProt O75469 · UniProt Q15788
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