Research workbench
Crystal structure of the ppargamma-lbd complexed with a cercosporamide derivative modulator cerco-a
Analyse Crystal structure of the ppargamma-lbd complexed with a cercosporamide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B1M
- Type
- protein
- Length
- 271 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peroxisome proliferator-activated…
- UniProt
- P37231, Q9UBK2
- Ligands
- KRC
- Pockets
- 1 · best druggability 0.77
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 | 260 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 11 | 64% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- KRC · (9aS)-8-acetyl-N-[(2-ethylnaphthalen-1-yl)methyl]-1,7-dihydroxy-3-methoxy-9a-methyl-9-oxo-9,9a-dihydrodibenzo[b,d]furan-4-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.77 | 0.85 | 50 | KRC |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3B1M · Crystal structure of the PPARgamma-LBD complexed with a cercosporamide derivative… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UBK2 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor gamma… · a predicted model of the same protein · chain B against A, TM-score 0.75
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 Q9UBK2
- Elsewhere: RCSB PDB 3B1M · PDBe 3B1M · UniProt P37231 · UniProt Q9UBK2
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