Research workbench
X-ray structure of human PPARalpha ligand binding domain-GW9662-ciprofibrate co-crystals obtained by delipidation and co-crystallization
Analyse X-ray structure of human PPARalpha ligand binding domain-GW9662-ciprofibrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L37
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.91
- Source
- Homo sapiens
- Molecule
- Peroxisome proliferator-activated receptor alpha
- UniProt
- Q07869
- Ligands
- GW9, C5F
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.91 · 2 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor alpha | protein | 270 | 66% helix, 4% strand | Q07869 |
| B | Peroxisome proliferator-activated receptor alpha | protein | 269 | 63% helix, 4% strand | Q07869 |
Ligands and binding sites
- GW9 · 2-chloro-5-nitro-N-phenylbenzamide · ligand · 6 copies · chains A, B
- C5F · 2-{4-[(1S)-2,2-dichlorocyclopropyl]phenoxy}-2-methylpropanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.85 | 0.87 | 60 | GW9, C5F |
| 2 | 708 | 0.84 | 0.87 | 64 | GW9, C5F |
| 3 | 112 | 0.39 | 0.75 | 19 | empty |
| 4 | 81 | 0.37 | 0.76 | 15 | empty |
| 5 | 91 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 620 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6L37 · X-ray structure of human pparalpha ligand binding domain-GW9662- ciprofibrate co-crystals… · 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 B against A, TM-score 0.98
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 6L37 · PDBe 6L37 · UniProt Q07869
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.