MolNFT v1 · #48850 · protein
Crystal structure of ppargamma bound to partial agonist ntzdpa
2Q5S · Peroxisome proliferator-activated receptor gamma: “Crystal structure of ppargamma bound to partial agonist ntzdpa”. X-ray diffraction, 1 ligand (NZA), 10 pockets (best druggability 0.83). MolNFT v1 #48850 on GenesisL1: 3D structure…
- PDB
- 2Q5S
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- NZA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 256 | 65% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 258 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- NZA · 5-chloro-1-(4-chlorobenzyl)-3-(phenylthio)-1H-indole-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.83 | 0.91 | 49 | NZA |
| 2 | 450 | 0.78 | 0.85 | 51 | NZA |
| 3 | 133 | 0.67 | 0.89 | 25 | empty |
| 4 | 107 | 0.61 | 0.87 | 26 | empty |
| 5 | 285 | 0.54 | 0.75 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1190 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2Q5S · Crystal Structure of PPARgamma bound to partial agonist nTZDpa · 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 2Q5S · PDBe 2Q5S · UniProt P37231
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