MolNFT v1 · #114025 · protein
Ternary complex of hpparalpha ligand binding domain, 17-oxodha and a SRC1 peptide
5AZT · Peroxisome proliferator-activated receptor alpha: “Ternary complex of hpparalpha ligand binding domain, 17-oxodha and a SRC1 peptide”. X-ray diffraction, 1 ligand (4M5), 4 pockets (best druggability 0.83). MolNFT v1 #114025 on…
- PDB
- 5AZT
- Type
- protein
- Length
- 523 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor alpha; 15-meric peptide from nuclear receptor…
- UniProt
- Q07869, Q15788
- Ligands
- 4M5
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor alpha | protein | 261 | 66% helix, 5% strand | Q07869 |
| B | Peroxisome proliferator-activated receptor alpha | protein | 251 | 69% helix, 5% strand | Q07869 |
| C | 15-meric peptide from nuclear receptor coactivator 1 | protein | 11 | 73% helix, 0% strand | Q15788 |
Ligands and binding sites
- 4M5 · (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.83 | 0.85 | 84 | 4M5 |
| 2 | 503 | 0.82 | 0.88 | 53 | 4M5 |
| 3 | 811 | 0.78 | 0.81 | 63 | empty |
| 4 | 91 | 0.47 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 521 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 419 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5AZT · Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide · 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 0.99
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 5AZT · PDBe 5AZT · UniProt Q07869 · UniProt Q15788
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