MolNFT v1 · #20405 · protein
Crystal structure of a new rexinoid bound to the rxralpha ligand binding doamin in the RXRALPHA/PPARGAMMA heterodimer
1RDT · Retinoic acid receptor rxr-alpha: “Crystal structure of a new rexinoid bound to the rxralpha ligand binding doamin in the RXRALPHA/PPARGAMMA…”. X-ray diffraction, 2 ligands (L79, 570), 10 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 1RDT
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Lxxll motif coactivator; Peroxisome proliferator…
- UniProt
- P19793, P37231
- Ligands
- L79, 570
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 211 | 70% helix, 3% strand | P19793 |
| B | Lxxll motif coactivator | protein | 9 | 78% helix, 0% strand | — |
| D | Peroxisome proliferator activated receptor gamma | protein | 253 | 68% helix, 5% strand | P37231 |
| E | Lxxll motif coactivator | protein | 7 | 71% helix, 0% strand | — |
Ligands and binding sites
- L79 · (S)-(2E)-3[4-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)tetrahydro-1-benzofuran-2-yl]-2-propenoic acid · ligand · chains A
- 570 · 2-(2-benzoyl-phenylamino)-3-{4-[2-(5-methyl-2-phenyl-oxazol-4-yl)-ethoxy]-phenyl}-propionic acid · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.83 | 0.95 | 31 | L79 |
| 2 | 476 | 0.82 | 0.88 | 50 | 570 |
| 3 | 266 | 0.57 | 0.78 | 34 | empty |
| 4 | 60 | 0.51 | 0.86 | 15 | empty |
| 5 | 59 | 0.47 | 0.84 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1182 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 261 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1RDT · Crystal Structure of a new rexinoid bound to the RXRalpha ligand binding doamin in the… · the same entry in another collection · chain D against D, TM-score 1.00
- P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain D against A, TM-score 0.99
- P19793 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P19793) · 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 P19793
- Every structure of UniProt P37231
- Elsewhere: RCSB PDB 1RDT · PDBe 1RDT · UniProt P19793 · UniProt P37231
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