Research workbench
Crystal structure of peroxisome proliferator-activated receptor gamma (pparg) and retinoic acid receptor alpha (rxra) in complex with 9-cis retinoic acid, co-activator peptide, and a partial agonist
Analyse Crystal structure of peroxisome proliferator-activated receptor gamma (pparg)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H0A
- Type
- protein
- Length
- 498 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…
- EC
- 2.3.1.48
- UniProt
- P19793, P37231, Q15788
- Ligands
- 9RA, D30
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 210 | 58% helix, 1% strand | P19793 |
| D | Peroxisome proliferator-activated receptor gamma | protein | 265 | 66% helix, 5% strand | P37231 |
| B | Nuclear receptor coactivator 1, co-activator peptide (EC 2.3.1.48) | protein | 11 | 0% helix, 0% strand | Q15788 |
| E | Nuclear receptor coactivator 1, co-activator peptide (EC 2.3.1.48) | protein | 12 | 67% helix, 0% strand | Q15788 |
Ligands and binding sites
- 9RA · 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydronaphthalen-2-yl)ethenyl]benzoic acid · ligand · chains A
- D30 · [(4-{[2-(pent-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}-5,6,7,8-tetrahydronaphthalen-1-yl)oxy]acetic 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.83 | 0.94 | 39 | 9RA |
| 2 | 567 | 0.83 | 0.88 | 55 | D30 |
| 3 | 334 | 0.69 | 0.83 | 51 | empty |
| 4 | 230 | 0.66 | 0.84 | 29 | empty |
| 5 | 60 | 0.63 | 0.93 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1170 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 563 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 365 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3H0A · Crystal Structure of Peroxisome Proliferator-Activated Receptor Gamma (PPARg) and… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q15788
- Elsewhere: RCSB PDB 3H0A · PDBe 3H0A · UniProt P19793 · UniProt P37231 · UniProt Q15788
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