Research workbench
Hppargamma ligand binding domain in complex with 5-oxo- tricosahexaenoic acid
Analyse Hppargamma ligand binding domain in complex with 5-oxo- tricosahexaenoic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X1H
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 5OX
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 256 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 254 | 70% helix, 5% strand | P37231 |
Ligands and binding sites
- 5OX · (7E,11Z,14Z,17Z,20Z)-5-oxotricosa-7,11,14,17,20-pentaenoic acid · ligand · 2 copies · chains A, B
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 | 542 | 0.83 | 0.88 | 63 | 5OX |
| 2 | 478 | 0.77 | 0.84 | 44 | 5OX |
| 3 | 483 | 0.62 | 0.76 | 45 | empty |
| 4 | 139 | 0.59 | 0.84 | 24 | empty |
| 5 | 120 | 0.56 | 0.84 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 964 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3X1H · hPPARgamma Ligand binding domain in complex with 5-oxo-tricosahexaenoic acid · 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 3X1H · PDBe 3X1H · UniProt P37231
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