Research workbench
Crystal structure of estrogen-related receptor gamma ligand-binding domain with DN200699
Analyse Crystal structure of estrogen-related receptor gamma ligand-binding domain with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KNR
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen-related receptor gamma
- UniProt
- P62508
- Ligands
- DL9
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen-related receptor gamma | protein | 222 | 68% helix, 3% strand | P62508 |
| B | Estrogen-related receptor gamma | protein | 225 | 66% helix, 4% strand | P62508 |
Ligands and binding sites
- DL9 · (E)-4-(1-(4-(1-cyclopropylpiperidin-4-yl)phenyl)-5-hydroxy-2-phenylpent-1-en-1-yl)phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.79 | 0.83 | 61 | DL9 |
| 2 | 590 | 0.79 | 0.84 | 59 | DL9 |
| 3 | 165 | 0.66 | 0.86 | 22 | empty |
| 4 | 181 | 0.63 | 0.84 | 26 | empty |
| 5 | 192 | 0.61 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1271 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6KNR · Crystal structure of Estrogen-related receptor gamma ligand-binding domain with DN200699 · 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 A against A, TM-score 0.96
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 6KNR · PDBe 6KNR · UniProt P62508
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