MolNFT v1 · #141388 · protein
Crystal structure of the ppargamma-lbd complexed with compound 13AB
5Z5S · Peroxisome proliferator-activated receptor gamma: “Crystal structure of the ppargamma-lbd complexed with compound 13AB”. X-ray diffraction, 2 ligands (RTE, CL), 2 pockets (best druggability 0.72). MolNFT v1 #141388 on GenesisL1: 3D…
- PDB
- 5Z5S
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Peptide from peroxisome…
- UniProt
- P37231, Q9UBK2
- Ligands
- RTE, CL
- Pockets
- 2 · best druggability 0.72
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 | 65% helix, 5% strand | P37231 |
| C | Peptide from peroxisome proliferator-activated receptor gamma coactivator 1-alpha | protein | 10 | 70% helix, 0% strand | Q9UBK2 |
Ligands and binding sites
- RTE · 3-{[6-(4-chloro-3-fluorophenoxy)-1-methyl-1H-benzimidazol-2-yl]methoxy}benzoic acid · ligand · chains A
- CL · Chloride ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.72 | 0.83 | 49 | RTE |
| 2 | 68 | 0.34 | 0.76 | 17 | CL |
Interfaces
1 interface between chains.
- A–C · 535 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Z5S · Crystal structure of the PPARgamma-LBD complexed with compound 13ab · 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 C against A, TM-score 0.81
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 5Z5S · PDBe 5Z5S · UniProt P37231 · UniProt Q9UBK2
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