Research workbench
Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR peptide and inverse agonist SR32904
Analyse Crystal structure of PPARgamma ligand-binding domain in complex with N-CoR… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8FKE
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.02
- Source
- Homo sapiens
- Molecule
- Peroxisome proliferator-activated receptor gamma; Nuclear receptor corepressor 1
- UniProt
- P37231, O75376
- Ligands
- Y5T
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.02 · 2 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 268 | 63% helix, 4% strand | P37231 |
| D | Nuclear receptor corepressor 1 | protein | 14 | 86% helix, 0% strand | O75376 |
Ligands and binding sites
- Y5T · 2-chloro-N-(2-methylpyridin-4-yl)-5-nitrobenzamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.72 | 0.83 | 37 | empty |
| 2 | 210 | 0.59 | 0.80 | 39 | Y5T |
Interfaces
1 interface between chains.
- A–D · 549 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- O75376 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 1 (O75376) · a predicted model of the same protein · chain D against A, TM-score 0.80
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
- Every structure of UniProt O75376
- Elsewhere: RCSB PDB 8FKE · PDBe 8FKE · UniProt P37231 · UniProt O75376
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