Research workbench
X-ray structure of human pparalpha ligand binding domain-bezafibrate- SRC1 coactivator peptide co-crystals obtained by soaking
Analyse X-ray structure of human pparalpha ligand binding domain-bezafibrate- SRC1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BPZ
- Type
- protein
- Length
- 543 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
- PEM
- Pockets
- 5 · best druggability 0.83
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 | 265 | 66% helix, 5% strand | Q07869 |
| B | 15-meric peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 11 | 73% helix, 0% strand | Q15788 |
| C | Peroxisome proliferator-activated receptor alpha | protein | 259 | 66% helix, 5% strand | Q07869 |
| D | 15-meric peptide from nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 8 | 63% helix, 0% strand | Q15788 |
Ligands and binding sites
- PEM · 2-[P-[2-P-chlorobenzamido)ethyl]phenoxy]-2-methylpropionic acid · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.83 | 0.88 | 59 | PEM |
| 2 | 687 | 0.82 | 0.86 | 69 | PEM |
| 3 | 270 | 0.53 | 0.75 | 34 | empty |
| 4 | 50 | 0.34 | 0.78 | 13 | empty |
| 5 | 53 | 0.25 | 0.73 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 630 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 462 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7BPZ · X-ray structure of human PPARalpha ligand binding domain-bezafibrate-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 0.99
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
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 7BPZ · PDBe 7BPZ · UniProt Q07869 · UniProt Q15788
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