MolNFT v1 · #174259 · protein
X-ray structure of human pparalpha ligand binding domain-clofibric acid-SRC1 coactivator peptide co-crystals obtained by delipidation and co-crystallization
7BPY · Peroxisome proliferator-activated receptor alpha: “X-ray structure of human pparalpha ligand binding domain-clofibric acid-SRC1 coactivator peptide co-crystals…”. X-ray diffraction, 1 ligand (E0O), 4 pockets (best druggability…
- PDB
- 7BPY
- Type
- protein
- Length
- 562 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor alpha; 15-meric peptide from nuclear receptor…
- EC
- 2.3.1.48
- UniProt
- Q07869, Q15788
- Ligands
- E0O
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor alpha | protein | 271 | 66% helix, 5% strand | Q07869 |
| B | 15-meric peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 14 | 57% helix, 0% strand | Q15788 |
| C | Peroxisome proliferator-activated receptor alpha | protein | 266 | 67% helix, 5% strand | Q07869 |
| D | 15-meric peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 55% helix, 0% strand | Q15788 |
Ligands and binding sites
- E0O · 2-(4-chloranylphenoxy)-2-methyl-propanoic acid · ligand · 4 copies · chains A, C
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 | 556 | 0.85 | 0.90 | 65 | E0O |
| 2 | 575 | 0.84 | 0.89 | 69 | E0O |
| 3 | 133 | 0.39 | 0.73 | 26 | empty |
| 4 | 78 | 0.32 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 728 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 615 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 279 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7BPY · X-ray structure of human PPARalpha ligand binding domain-clofibric acid-SRC1 coactivator… · 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 C 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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 7BPY · PDBe 7BPY · UniProt Q07869 · UniProt Q15788
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