Research workbench
Crystal structure of peroxisome proliferator-activatedeceptor alpha (pparalpha) complex with N-3-((2-(4-chlorophenyl)-5-methyl-1,3- oxazol-4-YL)METHOXY)BENZYL)-N-((4-METHYLPHENOXY)CARBONYL)GLYCINE
Analyse Crystal structure of peroxisome proliferator-activatedeceptor alpha (pparalpha)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KDU
- Type
- protein
- Length
- 535 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor alpha
- UniProt
- Q07869
- Ligands
- NKS
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor alpha | protein | 264 | 67% helix, 5% strand | Q07869 |
| B | Peroxisome proliferator-activated receptor alpha | protein | 271 | 67% helix, 5% strand | Q07869 |
Ligands and binding sites
- NKS · N-(3-{[2-(4-chlorophenyl)-5-methyl-1,3-oxazol-4-yl]methoxy}benzyl)-N-[(4-methylphenoxy)carbonyl]glycine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.84 | 0.89 | 63 | NKS |
| 2 | 940 | 0.83 | 0.84 | 94 | NKS |
| 3 | 52 | 0.29 | 0.75 | 13 | empty |
| 4 | 62 | 0.29 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 211 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KDU · Crystal structure of peroxisome proliferator-activatedeceptor alpha (PPARalpha) complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q07869 · AlphaFold monomer V2.0 prediction for peroxisome proliferator- activated receptor alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q07869
- Elsewhere: RCSB PDB 3KDU · PDBe 3KDU · UniProt Q07869
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