Research workbench
Crystal structure of human ppar-gamma ligand binding domain complex with a potency improved agonist
Analyse Crystal structure of human ppar-gamma ligand binding domain complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NOA
- Type
- protein
- Length
- 542 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 5BC
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor gamma | protein | 271 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- 5BC · (5-{3-[4-(biphenyl-4-ylcarbonyl)-2-propylphenoxy]propoxy}-1H-indol-1-yl)acetic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.85 | 0.89 | 68 | 5BC |
| 2 | 913 | 0.84 | 0.86 | 96 | 5BC |
| 3 | 610 | 0.73 | 0.80 | 63 | empty |
| 4 | 135 | 0.53 | 0.81 | 20 | empty |
| 5 | 86 | 0.43 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 870 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3NOA · Crystal structure of human PPAR-gamma ligand binding domain complex with a potency… · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 3NOA · PDBe 3NOA · UniProt P37231
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