MolNFT v2 · #220292 · protein
Crystal structure of pregnane X receptor ligand binding domain in complex with SJPYT-326
8SVR · Pregnane X receptor ligand binding domain fused to SRC-1…: “Crystal structure of pregnane X receptor ligand binding domain in complex with SJPYT-326”. X-ray diffraction at 2.92, 1 ligand (WT1), 4 pockets (best druggability 0.85).…
- PDB
- 8SVR
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.92
- Source
- Homo sapiens
- Molecule
- Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide
- EC
- 2.3.1.48
- UniProt
- O75469, Q15788
- Ligands
- WT1
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.92 · 2 distinct chains · 59% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide (EC 2.3.1.48) | protein | 282 | 58% helix, 8% strand | O75469, Q15788 |
| B | Pregnane X receptor ligand binding domain fused to SRC-1 coactivator peptide (EC 2.3.1.48) | protein | 278 | 61% helix, 8% strand | O75469, Q15788 |
Ligands and binding sites
- WT1 · (1P)-N-(5-tert-butyl-2-{[(3S)-hexan-3-yl]oxy}phenyl)-5-methyl-1-(2,4,5-trimethoxyphenyl)-1H-1,2,3-triazole-4-carboxamide · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.85 | 0.92 | 41 | WT1 |
| 2 | 658 | 0.83 | 0.87 | 71 | WT1 |
| 3 | 74 | 0.35 | 0.76 | 18 | empty |
| 4 | 66 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 824 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 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 0.94
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 8SVR · PDBe 8SVR · UniProt O75469 · UniProt Q15788
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.