MolNFT v1 · #156715 · protein
Crystal structure of human ppargamma ligand binding domain in complex with rosiglitazone and oleic acid
6MD4 · Peroxisome proliferator-activated receptor gamma: “Crystal structure of human ppargamma ligand binding domain in complex with rosiglitazone and oleic acid”. X-ray diffraction, 2 ligands (BRL, OLA), 7 pockets (best druggability…
- PDB
- 6MD4
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- BRL, OLA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 258 | 67% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 251 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · ligand · chains A
- OLA · Oleic acid · ligand · chains A
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 | 729 | 0.81 | 0.84 | 72 | empty |
| 2 | 475 | 0.79 | 0.86 | 50 | BRL, OLA |
| 3 | 313 | 0.58 | 0.77 | 25 | empty |
| 4 | 95 | 0.53 | 0.84 | 20 | empty |
| 5 | 171 | 0.45 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6MD4 · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with Rosiglitazone… · 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 6MD4 · PDBe 6MD4 · UniProt P37231
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