Research workbench
Crystal structure of the er-alpha ligand-binding domain (Y537S) in complex with the constrained way derivative, 4-(2-(3-methylbut-2-en- 1-yl)-7-(trifluoromethyl)-2H-indazol-3-YL)BENZENE-1,3-diol
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
- 5TLF
- Type
- protein
- Length
- 492 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
- 7EF
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 237 | 68% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 66% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | — |
| D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | — |
Ligands and binding sites
- 7EF · 4-[2-(3-methylbut-2-en-1-yl)-7-(trifluoromethyl)-2H-indazol-3-yl]benzene-1,3-diol · 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 | 191 | 0.84 | 0.97 | 26 | 7EF |
| 2 | 209 | 0.83 | 0.96 | 27 | 7EF |
| 3 | 96 | 0.65 | 0.90 | 18 | empty |
| 4 | 103 | 0.65 | 0.89 | 21 | empty |
| 5 | 280 | 0.55 | 0.76 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1714 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 497 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TLF · Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with the… · 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 B 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 5TLF · PDBe 5TLF · UniProt P03372
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