Research workbench
Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a phenylamino-substituted, methyl, triaryl-ethylene derivative 4,4'-{2-[3-(phenylamino)phenyl]prop-1-ene-1,1-diyl}diphenol
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
- 5DL4
- Type
- protein
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- 5C4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 237 | 71% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 240 | 69% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5C4 · 4,4'-{2-[3-(phenylamino)phenyl]prop-1-ene-1,1-diyl}diphenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.81 | 0.92 | 36 | 5C4 |
| 2 | 265 | 0.80 | 0.91 | 34 | 5C4 |
| 3 | 79 | 0.66 | 0.92 | 18 | empty |
| 4 | 74 | 0.64 | 0.92 | 18 | empty |
| 5 | 167 | 0.55 | 0.81 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1734 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 530 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DL4 · 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 B 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 5DL4 · PDBe 5DL4 · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.