Research workbench
Crystal structure of the estrogen receptor alpha ligand binding domain complexed with an oxabicyclic diarylethylene compound
Analyse Crystal structure of the estrogen receptor alpha ligand binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QH6
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q8BN74
- Ligands
- ODE
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 232 | 73% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 228 | 70% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q8BN74 |
Ligands and binding sites
- ODE · Diethyl (1R,2S,3R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.85 | 0.96 | 32 | ODE |
| 2 | 232 | 0.85 | 0.96 | 28 | ODE |
| 3 | 112 | 0.67 | 0.89 | 20 | empty |
| 4 | 96 | 0.60 | 0.87 | 17 | empty |
| 5 | 262 | 0.59 | 0.79 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1730 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 539 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2QH6 · Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain B 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 P03372
- Every structure of UniProt Q8BN74
- Elsewhere: RCSB PDB 2QH6 · PDBe 2QH6 · UniProt P03372 · UniProt Q8BN74
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