Research workbench
hPPARgamma Ligand binding domain in complex with 4-oxoDHA
Analyse hPPARgamma Ligand binding domain in complex with 4-oxoDHA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VV3
- Type
- protein
- Length
- 503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- HOMO SAPIENS
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- 4R8
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.85 · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 246 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- 4R8 · (6E,10Z,13Z,16Z,19Z)-4-oxodocosa-6,10,13,16,19-pentaenoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 502 | 0.78 | 0.85 | 48 | 4R8 |
| 2 | 557 | 0.76 | 0.83 | 58 | empty |
| 3 | 270 | 0.57 | 0.78 | 24 | empty |
| 4 | 205 | 0.53 | 0.78 | 28 | empty |
| 5 | 111 | 0.52 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 903 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 2VV3 · Hppargamma ligand binding domain in complex with 4-oxodha · the same entry in another collection · chain A against A, TM-score 1.00
- P37231 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 2VV3 · PDBe 2VV3 · UniProt P37231
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