Research workbench
Molecular recognition of nitro-fatty acids by ppar gamma
Analyse Molecular recognition of nitro-fatty acids by ppar gamma in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CWD
- Type
- protein
- Length
- 549 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; SRC1-2 peptide
- UniProt
- P37231, Q15788
- Ligands
- LNA, LNB
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 257 | 65% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 260 | 64% helix, 5% strand | P37231 |
| C, D | SRC1-2 peptide | protein | 16 | 56% helix, 0% strand | Q15788 |
Ligands and binding sites
- LNA · (9E,12Z)-10-nitrooctadeca-9,12-dienoic acid · ligand · 2 copies · chains A, B
- LNB · (9Z,12E)-12-nitrooctadeca-9,12-dienoic acid · ligand · 2 copies · chains A, B
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 | 770 | 0.83 | 0.85 | 66 | LNA, LNB |
| 2 | 524 | 0.81 | 0.87 | 57 | LNA, LNB |
| 3 | 709 | 0.71 | 0.78 | 79 | empty |
| 4 | 79 | 0.39 | 0.77 | 14 | empty |
| 5 | 65 | 0.39 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 815 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 737 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 699 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3CWD · Molecular recognition of nitro-fatty acids by PPAR gamma · 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 3CWD · PDBe 3CWD · UniProt P37231 · UniProt Q15788
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