Research workbench
Estrogen receptor beta ligand binding domain in complex with a benzopyran agonist
Analyse Estrogen receptor beta ligand binding domain in complex with a benzopyran… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JJ3
- Type
- protein
- Length
- 449 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor beta
- UniProt
- Q92731
- Ligands
- JJ3
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor beta | protein | 223 | 71% helix, 4% strand | Q92731 |
| B | Estrogen receptor beta | protein | 226 | 73% helix, 4% strand | Q92731 |
Ligands and binding sites
- JJ3 · (3as,4r,9br)-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3A,4,9B-hexahydrocyclopenta[c]chromen-8-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.84 | 0.97 | 22 | JJ3 |
| 2 | 167 | 0.83 | 0.97 | 21 | JJ3 |
| 3 | 137 | 0.59 | 0.84 | 23 | empty |
| 4 | 184 | 0.59 | 0.82 | 28 | empty |
| 5 | 244 | 0.57 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1654 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2JJ3 · Estrogen receptor beta ligand binding domain in complex with a Benzopyran agonist · the same entry in another collection · chain A against A, TM-score 1.00
- Q92731 · AlphaFold monomer V2.0 prediction for estrogen receptor beta (Q92731) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q92731
- Elsewhere: RCSB PDB 2JJ3 · PDBe 2JJ3 · UniProt Q92731
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