Research workbench
X-ray crystal structure of the ppargamma ligand binding domain in complex with rivoglitazone
Analyse X-ray crystal structure of the ppargamma ligand binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U5L
- Type
- protein
- Length
- 513 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 7VA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 259 | 65% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 254 | 66% helix, 5% strand | P37231 |
Ligands and binding sites
- 7VA · (5S)-5-({4-[(6-methoxy-1-methyl-1H-benzimidazol-2-yl) methoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.84 | 0.92 | 52 | empty |
| 2 | 458 | 0.80 | 0.87 | 54 | 7VA |
| 3 | 299 | 0.59 | 0.78 | 35 | empty |
| 4 | 291 | 0.55 | 0.76 | 29 | empty |
| 5 | 115 | 0.52 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 983 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5U5L · X-ray Crystal Structure of the PPARgamma Ligand Binding Domain in Complex with… · 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
- Elsewhere: RCSB PDB 5U5L · PDBe 5U5L · UniProt P37231
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