MolNFT v1 · #48379 · protein
Ligand-binding domain of the human peroxisome proliferator activated receptor gamma
2PRG: “Ligand-binding domain of the human peroxisome proliferator activated receptor gamma”. X-ray diffraction, 1 ligand (BRL), 10 pockets (best druggability 0.83). MolNFT v1 #48379 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2PRG
- Type
- protein
- Length
- 549 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator activated receptor gamma; Nuclear receptor coactivator src-1
- UniProt
- P37231, O43792
- Ligands
- BRL
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator activated receptor gamma | protein | 271 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator activated receptor gamma | protein | 246 | 71% helix, 4% strand | P37231 |
| C | Nuclear receptor coactivator src-1 | protein | 32 | 50% helix, 0% strand | O43792 |
Ligands and binding sites
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.83 | 0.86 | 71 | BRL |
| 2 | 361 | 0.79 | 0.88 | 40 | BRL |
| 3 | 143 | 0.57 | 0.82 | 21 | empty |
| 4 | 104 | 0.52 | 0.83 | 20 | empty |
| 5 | 119 | 0.52 | 0.81 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1110 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 744 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 631 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2PRG · Ligand-binding domain of the human peroxisome proliferator activated receptor gamma · 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 P37231
- Every structure of UniProt O43792
- Elsewhere: RCSB PDB 2PRG · PDBe 2PRG · UniProt P37231 · UniProt O43792
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