Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with 2,5-BIS(2-fluoro-4-HYDROXYPHENYL)THIOPHENE 1-oxide
Analyse Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TM1
- Type
- protein
- Length
- 463 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
- 7EQ
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 220 | 70% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 226 | 69% helix, 3% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 8 | 75% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 7EQ · 2,5-bis(2-fluoro-4-hydroxyphenyl)-1H-1lambda~4~-thiophen-1-one · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.83 | 0.96 | 21 | 7EQ |
| 2 | 188 | 0.81 | 0.95 | 21 | 7EQ |
| 3 | 82 | 0.64 | 0.91 | 17 | empty |
| 4 | 81 | 0.61 | 0.89 | 16 | empty |
| 5 | 272 | 0.57 | 0.77 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1620 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 460 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5TM1 · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with… · 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 5TM1 · PDBe 5TM1 · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.