MolNFT v1 · #57497 · protein
Crystal structure of a mixed agonist-bound rar-alpha and antagonist- bound rxr-alpha heterodimer ligand binding domains
3A9E · Retinoic acid receptor rxr-alpha: “Crystal structure of a mixed agonist-bound rar-alpha and antagonist- bound rxr-alpha heterodimer ligand…”. X-ray diffraction, 2 ligands (754, REA), 5 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3A9E
- Type
- protein
- Length
- 468 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Retinoic acid receptor alpha; 13-mer (lxxll motif) from…
- UniProt
- P28700, P10276, Q15596
- Ligands
- 754, REA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 218 | 67% helix, 3% strand | P28700 |
| B | Retinoic acid receptor alpha | protein | 239 | 67% helix, 4% strand | P10276 |
| I | 13-mer (lxxll motif) from nuclear receptor coactivator 2 | protein | 11 | 73% helix, 0% strand | Q15596 |
Ligands and binding sites
- 754 · (2E,4E,6Z)-3-methyl-7-(5,5,8,8-tetramethyl-3-propoxy-5, 6,7,8-tetrahydronaphthalen-2-yl)octa-2,4,6-trienoic acid · ligand · chains A
- REA · Retinoic acid · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.82 | 0.93 | 36 | REA |
| 2 | 312 | 0.76 | 0.87 | 36 | 754 |
| 3 | 661 | 0.70 | 0.78 | 70 | empty |
| 4 | 94 | 0.49 | 0.82 | 20 | empty |
| 5 | 95 | 0.43 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 879 Ų buried · 7 hydrogen bonds · protein-protein
- B–I · 502 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3A9E · Crystal structure of a mixed agonist-bound RAR-alpha and antagonist-bound RXR-alpha… · the same entry in another collection · chain A against A, TM-score 1.00
- P10276 · AlphaFold monomer V2.0 prediction for retinoic acid receptor alpha (P10276) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P28700 · AlphaFold monomer V2.0 prediction for retinoic acid receptor rxr- alpha (P28700) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P28700
- Every structure of UniProt P10276
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3A9E · PDBe 3A9E · UniProt P28700 · UniProt P10276 · UniProt Q15596
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