Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with a dichloro-substituted, 3-methyl 2,5-diarylthiophene-core ligand 4,4'-(3-methylthiene-2,5-DIYL)BIS(3-chlorophenol)
Analyse Crystal structure of the er-alpha ligand-binding domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DRJ
- Type
- protein
- Length
- 496 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372
- Ligands
- 5EU
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 234 | 65% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 242 | 66% helix, 3% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- 5EU · 4,4'-(3-methylthiene-2,5-diyl)bis(3-chlorophenol) · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.83 | 0.96 | 26 | 5EU |
| 2 | 282 | 0.82 | 0.93 | 34 | 5EU |
| 3 | 76 | 0.62 | 0.90 | 15 | empty |
| 4 | 80 | 0.60 | 0.88 | 17 | empty |
| 5 | 89 | 0.50 | 0.83 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1703 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 531 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 521 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DRJ · Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a… · 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 A against A, TM-score 0.98
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
- Elsewhere: RCSB PDB 5DRJ · PDBe 5DRJ · UniProt P03372
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