Research workbench
Crystal structure of the SR12813-bound PXR/RXRALPHA lbd heterotetramer complex
Analyse Crystal structure of the SR12813-bound PXR/RXRALPHA lbd heterotetramer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J5X
- Type
- protein
- Length
- 1,063 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha, nuclear receptor coactivator 1; Nuclear receptor…
- EC
- 2.3.1.48
- UniProt
- P19793, Q15788, O75469
- Ligands
- SRL
- Pockets
- 19 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Retinoic acid receptor rxr-alpha, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 239 | 66% helix, 2% strand | P19793, Q15788 |
| C | Retinoic acid receptor rxr-alpha, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 238 | 64% helix, 2% strand | P19793, Q15788 |
| A | Nuclear receptor subfamily 1 group I member 2, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 293 | 57% helix, 6% strand | Q15788, O75469 |
| B | Nuclear receptor subfamily 1 group I member 2, nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 293 | 55% helix, 6% strand | Q15788, O75469 |
Ligands and binding sites
- SRL · [2-(3,5-di-tert-butyl-4-hydroxy-phenyl)-1-(diethoxy-phosphoryl)-vinyl]-phosphonic acid diethlyl ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.87 | 0.93 | 46 | SRL |
| 2 | 585 | 0.87 | 0.92 | 45 | SRL |
| 3 | 221 | 0.85 | 0.97 | 41 | empty |
| 4 | 199 | 0.84 | 0.97 | 35 | empty |
| 5 | 490 | 0.67 | 0.78 | 47 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1338 Ų buried · 12 hydrogen bonds · protein-protein
- D–A · 1334 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 782 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4J5X · Crystal Structure of the SR12813-bound PXR/RXRalpha LBD Heterotetramer Complex · the same entry in another collection · chain D against D, 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 0.93
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 P19793
- Every structure of UniProt Q15788
- Every structure of UniProt O75469
- Elsewhere: RCSB PDB 4J5X · PDBe 4J5X · UniProt P19793 · UniProt Q15788 · UniProt O75469
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