Research workbench
Crystal structure of estrogen related receptor-3 (err-gamma) ligand binding domain with DN200434
Analyse Crystal structure of estrogen related receptor-3 (err-gamma) ligand binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YSO
- Type
- protein
- Length
- 650 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen-related receptor gamma
- UniProt
- P62508
- Ligands
- 90C
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen-related receptor gamma | protein | 222 | 68% helix, 4% strand | P62508 |
| B | Estrogen-related receptor gamma | protein | 224 | 65% helix, 3% strand | P62508 |
| C | Estrogen-related receptor gamma | protein | 204 | 67% helix, 3% strand | P62508 |
Ligands and binding sites
- 90C · 4-[5-oxidanyl-2-phenyl-1-[4-(4-propan-2-ylpiperazin-1-yl)phenyl]pent-1-enyl]phenol · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.79 | 0.91 | 31 | 90C |
| 2 | 253 | 0.78 | 0.90 | 29 | 90C |
| 3 | 619 | 0.75 | 0.81 | 68 | empty |
| 4 | 320 | 0.74 | 0.86 | 30 | 90C |
| 5 | 182 | 0.67 | 0.86 | 26 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1288 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YSO · Crystal structure of Estrogen Related Receptor-3 (ERR-gamma) ligand binding domain with… · the same entry in another collection · chain A against A, TM-score 1.00
- P62508 · AlphaFold monomer V2.0 prediction for estrogen-related receptor gamma (P62508) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P62508
- Elsewhere: RCSB PDB 5YSO · PDBe 5YSO · UniProt P62508
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