Research workbench
Crystal structure of ppar gamma ligand binding domain in complex with a novel partial agonist gq-16
Analyse Crystal structure of ppar gamma ligand binding domain in complex with a novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T03
- Type
- protein
- Length
- 535 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Nuclear receptor coactivator 1
- EC
- 2.3.1.48
- UniProt
- P37231, Q15788
- Ligands
- 3T0
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 265 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 249 | 63% helix, 5% strand | P37231 |
| C | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 8 | 75% helix, 0% strand | Q15788 |
| D | Nuclear receptor coactivator 1 (EC 2.3.1.48) | protein | 13 | 69% helix, 0% strand | Q15788 |
Ligands and binding sites
- 3T0 · (5Z)-5-(5-bromo-2-methoxybenzylidene)-3-(4-methylbenzyl)-1,3-thiazolidine-2,4-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.79 | 0.83 | 66 | 3T0 |
| 2 | 425 | 0.77 | 0.85 | 52 | 3T0 |
| 3 | 736 | 0.73 | 0.79 | 73 | empty |
| 4 | 53 | 0.43 | 0.83 | 14 | empty |
| 5 | 67 | 0.34 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 767 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 639 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 539 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3T03 · Crystal structure of PPAR gamma ligand binding domain in complex with a novel partial… · 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 P37231
- Every structure of UniProt Q15788
- Elsewhere: RCSB PDB 3T03 · PDBe 3T03 · UniProt P37231 · UniProt Q15788
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