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Structure of human pregnane X receptor ligand binding domain bound tethered with src co-activator peptide in complex with (S,S)-1
Analyse Structure of human pregnane X receptor ligand binding domain bound tethered… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XP9
- Type
- protein
- Length
- 531 residues
- Chains
- 2
- 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 fusion
- EC
- 2.3.1.48
- UniProt
- O75469, Q15788
- Ligands
- QCG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2,NUCLEAR receptor coactivator 1 fusion (EC 2.3.1.48) | protein | 266 | 62% helix, 8% strand | O75469, Q15788 |
| B | Nuclear receptor subfamily 1 group I member 2,NUCLEAR receptor coactivator 1 fusion (EC 2.3.1.48) | protein | 265 | 60% helix, 8% strand | O75469, Q15788 |
Ligands and binding sites
- QCG · (2S)-tert-butoxy[7-(8-fluoro-5-methyl-3,4-dihydro-2H-1-benzopyran-6-yl)-5-methyl-2-phenylpyrazolo[1,5-a]pyrimidin-6-yl]acetic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 697 | 0.79 | 0.82 | 43 | QCG |
| 2 | 529 | 0.74 | 0.81 | 37 | QCG |
| 3 | 73 | 0.34 | 0.76 | 14 | empty |
| 4 | 51 | 0.31 | 0.77 | 15 | empty |
| 5 | 67 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 737 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6XP9 · STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC… · 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 0.94
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 6XP9 · PDBe 6XP9 · UniProt O75469 · UniProt Q15788
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