Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with (E)-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
- 5TN8
- Type
- protein
- Length
- 481 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
- 7G3
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 228 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 70% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 67% helix, 0% strand | Q15596 |
Ligands and binding sites
- 7G3 · 3-[(Z)-(hydroxyimino)methyl][1,1'-biphenyl]-4,4'-diol · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.82 | 0.97 | 22 | 7G3 |
| 2 | 135 | 0.82 | 0.98 | 20 | 7G3 |
| 3 | 79 | 0.66 | 0.92 | 20 | empty |
| 4 | 80 | 0.65 | 0.91 | 17 | empty |
| 5 | 301 | 0.63 | 0.80 | 36 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1696 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 501 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5TN8 · 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 5TN8 · PDBe 5TN8 · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.