Research workbench
Human ppargamma ligand-binding domain in complex with indomethacin and nitro-233
Analyse Human ppargamma ligand-binding domain in complex with indomethacin and nitro-233 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ADX
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- IMN, NRO
- Pockets
- 11 · best druggability 0.85
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 | 274 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 251 | 71% helix, 5% strand | P37231 |
Ligands and binding sites
- IMN · Indomethacin · ligand · 2 copies · chains A, B
- NRO · 3-[5-(2-nitropent-1-en-1-yl)furan-2-yl]benzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.85 | 0.91 | 58 | NRO, IMN |
| 2 | 490 | 0.79 | 0.86 | 52 | IMN |
| 3 | 125 | 0.60 | 0.86 | 17 | empty |
| 4 | 139 | 0.57 | 0.83 | 24 | empty |
| 5 | 224 | 0.55 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3ADX · Human PPARgamma ligand-binding domain in complex with indomethacin and nitro-233 · 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 3ADX · PDBe 3ADX · UniProt P37231
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