Research workbench
X-ray structure of human pparalpha ligand binding domain-GW9662- gemfibrozil co-crystals obtained by delipidation and co- crystallization
Analyse X-ray structure of human pparalpha ligand binding domain-GW9662- gemfibrozil… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L38
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor alpha
- UniProt
- Q07869
- Ligands
- GW9
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisome proliferator-activated receptor alpha | protein | 270 | 66% helix, 5% strand | Q07869 |
Ligands and binding sites
- GW9 · 2-chloro-5-nitro-N-phenylbenzamide · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.85 | 0.88 | 66 | GW9 |
| 2 | 718 | 0.83 | 0.86 | 62 | GW9 |
| 3 | 76 | 0.35 | 0.76 | 15 | empty |
| 4 | 72 | 0.34 | 0.75 | 17 | empty |
| 5 | 80 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6L38 · X-ray structure of human PPARalpha ligand binding domain-GW9662-gemfibrozil 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 A 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 6L38 · PDBe 6L38 · UniProt Q07869
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