Research workbench
Hppargamma ligand binding domain in complex with 5-hepa
Analyse Hppargamma ligand binding domain in complex with 5-hepa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VV2
- 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
- 5HE
- Pockets
- 8 · best druggability 0.83
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 | 256 | 68% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 257 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- 5HE · (5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid · ligand · 3 copies · chains A, B
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 | 698 | 0.83 | 0.87 | 61 | 5HE |
| 2 | 512 | 0.78 | 0.85 | 51 | 5HE |
| 3 | 491 | 0.62 | 0.75 | 44 | empty |
| 4 | 124 | 0.54 | 0.82 | 22 | empty |
| 5 | 264 | 0.53 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 909 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2VV2 · hPPARgamma Ligand binding domain in complex with 5-HEPA · the same entry in another collection · chain B against B, 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 2VV2 · PDBe 2VV2 · UniProt P37231
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