Research workbench
Human ppardelta ligand-binding domain in complexed with specific agonist 3
Analyse Human ppardelta ligand-binding domain in complexed with specific agonist 3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U3S
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor delta
- UniProt
- Q03181
- Ligands
- 7V4, B7G, K
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor delta | protein | 271 | 68% helix, 5% strand | Q03181 |
| B | Peroxisome proliferator-activated receptor delta | protein | 263 | 67% helix, 5% strand | Q03181 |
Ligands and binding sites
- 7V4 · 6-[2-({[4-(furan-3-yl)benzene-1-carbonyl](propan-2-yl) amino}methyl)phenoxy]hexanoic acid · ligand · 2 copies · chains A, B
- B7G · heptyl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.86 | 0.92 | 53 | 7V4, PGO |
| 2 | 582 | 0.85 | 0.90 | 54 | 7V4, PGO |
| 3 | 436 | 0.75 | 0.84 | 46 | B7G |
| 4 | 62 | 0.40 | 0.80 | 12 | empty |
| 5 | 80 | 0.33 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 730 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5U3S · Human PPARdelta ligand-binding domain in complexed with specific agonist 3 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q03181
- Elsewhere: RCSB PDB 5U3S · PDBe 5U3S · UniProt Q03181
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