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Structure of human pregnane X receptor ligand binding domain bound with adnectin-1 and compound-1
Analyse Structure of human pregnane X receptor ligand binding domain bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S0T
- Type
- protein
- Length
- 744 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2; Adnectin-1
- UniProt
- O75469
- Ligands
- 40U
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2 | protein | 279 | 58% helix, 8% strand | O75469 |
| B | Nuclear receptor subfamily 1 group I member 2 | protein | 283 | 58% helix, 8% strand | O75469 |
| D, E | Adnectin-1 | protein | 91 | 0% helix, 47% strand | — |
Ligands and binding sites
- 40U · N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-2-cyclopropylacetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.86 | 0.93 | 44 | 40U |
| 2 | 506 | 0.85 | 0.91 | 44 | 40U |
| 3 | 403 | 0.59 | 0.75 | 45 | empty |
| 4 | 322 | 0.57 | 0.76 | 36 | empty |
| 5 | 314 | 0.55 | 0.75 | 56 | empty |
Interfaces
4 interfaces between chains.
- B–E · 734 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 629 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 127 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4S0T · Structure of human pregnane X receptor ligand binding domain bound with adnectin-1 and… · 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 0.97
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
- Elsewhere: RCSB PDB 4S0T · PDBe 4S0T · UniProt O75469
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