Research workbench
Crystal structure of human ppargamma ligand binding domain in complex with GW9662 and arachidonic acid
Analyse Crystal structure of human ppargamma ligand binding domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MD2
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- GW9, ACD
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 255 | 69% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 257 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- GW9 · 2-chloro-5-nitro-N-phenylbenzamide · ligand · 2 copies · chains A, B
- ACD · Arachidonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.81 | 0.83 | 73 | GW9, ACD |
| 2 | 523 | 0.80 | 0.86 | 50 | GW9, ACD |
| 3 | 138 | 0.59 | 0.84 | 20 | empty |
| 4 | 100 | 0.57 | 0.86 | 19 | empty |
| 5 | 225 | 0.51 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 928 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MD2 · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and… · 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 6MD2 · PDBe 6MD2 · UniProt P37231
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