Research workbench
Crystal structure of ppargamma ligand binding domain in complex with N-cor peptide and inverse agonist T0070907
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
- 6ONI
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Ncor isoform C
- UniProt
- P37231, Q86YY1
- Ligands
- EEY
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Peroxisome proliferator-activated receptor gamma | protein | 261 | 67% helix, 5% strand | P37231 |
| D | Ncor isoform C | protein | 13 | 77% helix, 0% strand | Q86YY1 |
Ligands and binding sites
- EEY · 2-chloro-5-nitro-N-(pyridin-4-yl)benzamide · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.70 | 0.83 | 33 | empty |
| 2 | 167 | 0.57 | 0.81 | 35 | EEY |
| 3 | 63 | 0.40 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- B–D · 539 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6ONI · Crystal structure of PPARgamma ligand binding domain in complex with N-CoR peptide and… · 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
- Every structure of UniProt Q86YY1
- Elsewhere: RCSB PDB 6ONI · PDBe 6ONI · UniProt P37231 · UniProt Q86YY1
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