MolNFT v1 · #123376 · protein
Ppargamma-RXRALPHA(S427F) heterodimer in complex with src-1, rosiglitazone, and 9-cis-retanoic acid
5JI0 · Retinoic acid receptor rxr-alpha: “Ppargamma-RXRALPHA(S427F) heterodimer in complex with src-1, rosiglitazone, and 9-cis-retanoic acid”. X-ray diffraction, 2 ligands (9CR, BRL), 7 pockets (best druggability 0.82). MolNFT v1 #123376…
- PDB
- 5JI0
- Type
- protein
- Length
- 513 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
- 9CR, BRL
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 216 | 66% helix, 3% strand | P19793 |
| D | Peroxisome proliferator-activated receptor gamma | protein | 269 | 64% helix, 5% strand | P37231 |
| E | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 19 | 63% helix, 0% strand | Q15788 |
| F | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 9 | 78% helix, 0% strand | Q15788 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · chains A
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.82 | 0.91 | 44 | 9CR |
| 2 | 565 | 0.79 | 0.85 | 60 | BRL |
| 3 | 248 | 0.55 | 0.77 | 35 | empty |
| 4 | 104 | 0.45 | 0.79 | 17 | empty |
| 5 | 70 | 0.35 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1263 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 749 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 501 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5JI0 · PPARgamma-RXRalpha(S427F) heterodimer in complex with SRC-1, rosiglitazone, 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 5JI0 · PDBe 5JI0 · UniProt P19793 · UniProt P37231 · UniProt Q15788
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