Research workbench
The crystal structure of the human pparaplpha ligand binding domain in complex with a a-hydroxyimino phenylpropanoic acid
Analyse The crystal structure of the human pparaplpha ligand binding domain in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NPA
- Type
- protein
- Length
- 561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor alpha; Src- peptide from nuclear receptor…
- UniProt
- Q07869, Q2T9G5
- Ligands
- MMB
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor alpha | protein | 269 | 68% helix, 4% strand | Q07869 |
| B | Src- peptide from nuclear receptor coactivator 1 | protein | 15 | 53% helix, 0% strand | Q2T9G5 |
| C | Peroxisome proliferator-activated receptor alpha | protein | 267 | 67% helix, 5% strand | Q07869 |
| D | Src- peptide from nuclear receptor coactivator 1 | protein | 10 | 60% helix, 0% strand | Q2T9G5 |
Ligands and binding sites
- MMB · (2R,3E)-2-{4-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]benzyl}-3-(propoxyimino)butanoic 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.85 | 0.90 | 57 | MMB |
| 2 | 570 | 0.84 | 0.89 | 59 | MMB |
| 3 | 165 | 0.45 | 0.75 | 22 | empty |
| 4 | 82 | 0.38 | 0.77 | 16 | empty |
| 5 | 95 | 0.34 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 716 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 633 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 590 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2NPA · the crystal structure of the human PPARaplpha ligand binding domain in complex with a… · 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 Q2T9G5
- Elsewhere: RCSB PDB 2NPA · PDBe 2NPA · UniProt Q07869 · UniProt Q2T9G5
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