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Crystal structure of human ppargamma ligand binding domain in complex with T0070907
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
- 6C1I
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- EEY, KNA
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 263 | 65% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 258 | 67% helix, 5% strand | P37231 |
Ligands and binding sites
- EEY · 2-chloro-5-nitro-N-(pyridin-4-yl)benzamide · ligand · 2 copies · chains A, B
- KNA · nonanoic 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.84 | 0.88 | 65 | EEY, KNA |
| 2 | 512 | 0.83 | 0.89 | 53 | EEY, KNA |
| 3 | 472 | 0.67 | 0.79 | 38 | empty |
| 4 | 326 | 0.58 | 0.76 | 33 | empty |
| 5 | 100 | 0.50 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 958 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6C1I · Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with T0070907 · 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 6C1I · PDBe 6C1I · UniProt P37231
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