Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with a dimethyl-substituted, 3,4-diarylthiophene dioxide core ligand
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
- 5DTV
- Type
- protein
- Length
- 486 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- 5FS
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 230 | 68% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
| B | Estrogen receptor | protein | 238 | 62% helix, 3% strand | P03372 |
Ligands and binding sites
- 5FS · 3,4-bis(4-hydroxy-2-methylphenyl)-1H-1lambda~6~-thiophene-1,1-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.85 | 0.97 | 22 | 5FS |
| 2 | 179 | 0.83 | 0.97 | 22 | 5FS |
| 3 | 547 | 0.67 | 0.78 | 54 | empty |
| 4 | 81 | 0.62 | 0.89 | 16 | empty |
| 5 | 82 | 0.61 | 0.89 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1663 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 492 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 474 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5DTV · 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 0.99
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 Q15596
- Elsewhere: RCSB PDB 5DTV · PDBe 5DTV · UniProt P03372 · UniProt Q15596
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