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The 2.1 ångström resolution crystal structure of the heterodimer of the human rxralpha and ppargamma ligand binding domains respectively bound with 9-cis retinoic acid and GI262570 and co-activator peptides.
Analyse The 2.1 ångström resolution crystal structure of the heterodimer of the human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FM9
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Peroxisome proliferator activated receptor gamma…
- UniProt
- P19793, P37231, O43793
- Ligands
- 9CR, 570
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 232 | 59% helix, 3% strand | P19793 |
| D | Peroxisome proliferator activated receptor gamma | protein | 272 | 67% helix, 5% strand | P37231 |
| B | Steroid receptor coactivator | protein | 10 | 70% helix, 0% strand | O43793 |
| E | Steroid receptor coactivator | protein | 16 | 50% helix, 0% strand | O43793 |
Ligands and binding sites
- 9CR · (9cis)-retinoic 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.84 | 0.88 | 68 | 570 |
| 2 | 311 | 0.84 | 0.93 | 45 | 9CR |
| 3 | 405 | 0.67 | 0.80 | 42 | empty |
| 4 | 136 | 0.47 | 0.78 | 20 | empty |
| 5 | 88 | 0.41 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1209 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 641 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 550 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1FM9 · The 2.1 ångström resolution crystal structure of the heterodimer of the human rxralpha… · 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 0.97
- 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 0.94
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 P19793
- Every structure of UniProt P37231
- Every structure of UniProt O43793
- Elsewhere: RCSB PDB 1FM9 · PDBe 1FM9 · UniProt P19793 · UniProt P37231 · UniProt O43793
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