Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with (E)-3'-fluoro-4'-hydroxy-3-((HYDROXYIMINIO)METHYL)-[1, 1'-biphenyl]-4-olate
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
- 5TN7
- Type
- protein
- Length
- 489 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
- 7G2
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 236 | 67% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 69% helix, 3% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 7G2 · 3-fluoro-3'-[(E)-(hydroxyimino)methyl][1,1'-biphenyl]-4,4'-diol · ligand · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.83 | 0.97 | 21 | 7G2 |
| 2 | 153 | 0.81 | 0.97 | 21 | 7G2 |
| 3 | 92 | 0.64 | 0.90 | 19 | empty |
| 4 | 88 | 0.62 | 0.89 | 16 | empty |
| 5 | 333 | 0.58 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1700 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 511 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5TN7 · 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 5TN7 · PDBe 5TN7 · UniProt P03372 · UniProt Q15596
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