Research workbench
Human ppar gamma ligand binding domain in complex with MCC555
Analyse Human ppar gamma ligand binding domain in complex with MCC555 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B0Q
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- MC5
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 262 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 245 | 70% helix, 5% strand | P37231 |
Ligands and binding sites
- MC5 · (5S)-5-({6-[(2-fluorobenzyl)oxy]naphthalen-2-yl}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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 442 | 0.76 | 0.85 | 50 | MC5 |
| 2 | 577 | 0.76 | 0.82 | 55 | empty |
| 3 | 615 | 0.70 | 0.79 | 67 | empty |
| 4 | 85 | 0.59 | 0.88 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1062 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3B0Q · Human PPAR gamma ligand binding domain in complex with MCC555 · 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 3B0Q · PDBe 3B0Q · UniProt P37231
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