Research workbench
The X-ray crystal structure of ppar-gamma in complex with an indole derivative modulator, GSK538, and an src-1 peptide
Analyse The X-ray crystal structure of ppar-gamma in complex with an indole derivative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMG
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Steroid receptor coactivator-1
- UniProt
- P37231
- Ligands
- 538
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 259 | 67% helix, 5% strand | P37231 |
| B | Steroid receptor coactivator-1 | protein | 11 | 64% helix, 0% strand | — |
| D | Peroxisome proliferator-activated receptor gamma | protein | 256 | 66% helix, 5% strand | P37231 |
| E | Steroid receptor coactivator-1 | protein | 18 | 50% helix, 0% strand | — |
Ligands and binding sites
- 538 · 4'-[(2,3-dimethyl-5-{[(1S)-1-phenylpropyl]carbamoyl}-1H-indol-1-yl)methyl]biphenyl-2-carboxylic acid · ligand · 2 copies · chains A, D
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 | 626 | 0.83 | 0.87 | 55 | 538 |
| 2 | 551 | 0.81 | 0.86 | 58 | 538 |
| 3 | 787 | 0.75 | 0.79 | 82 | empty |
| 4 | 73 | 0.35 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 796 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 655 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 576 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3KMG · The X-ray Crystal Structure of PPAR-gamma in Complex with an Indole Derivative Modulator… · 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
- Elsewhere: RCSB PDB 3KMG · PDBe 3KMG · UniProt P37231
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