Research workbench
Crystal structure of ppargamma ligand binding domain in complex with smrt peptide and inverse agonist T0070907
Analyse Crystal structure of ppargamma ligand binding domain in complex with smrt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDZ
- Type
- protein
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Nuclear receptor corepressor 2
- UniProt
- P37231, Q9Y618
- Ligands
- EEY
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Peroxisome proliferator-activated receptor gamma | protein | 262 | 66% helix, 5% strand | P37231 |
| C | Nuclear receptor corepressor 2 | protein | 13 | 77% helix, 0% strand | Q9Y618 |
| A | Peroxisome proliferator-activated receptor gamma | protein | 256 | 66% helix, 5% strand | P37231 |
| D | Nuclear receptor corepressor 2 | protein | 12 | 83% helix, 0% strand | Q9Y618 |
Ligands and binding sites
- EEY · 2-chloro-5-nitro-N-(pyridin-4-yl)benzamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.78 | 0.92 | 28 | empty |
| 2 | 789 | 0.75 | 0.79 | 104 | EEY |
| 3 | 311 | 0.72 | 0.84 | 32 | empty |
| 4 | 184 | 0.60 | 0.82 | 24 | empty |
| 5 | 124 | 0.44 | 0.77 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1023 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6PDZ · Crystal structure of PPARgamma ligand binding domain in complex with SMRT peptide and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y618 · AlphaFold monomer V2.0 prediction for nuclear receptor corepressor 2 (Q9Y618) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q9Y618
- Elsewhere: RCSB PDB 6PDZ · PDBe 6PDZ · UniProt P37231 · UniProt Q9Y618
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