Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with a resorcinyl 2-chloro-substituted diaryl-imine analog 4-[(E)- [(2-CHLOROPHENYL)IMINO](4-HYDROXYPHENYL)METHYL]BENZENE-1,3-diol
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
- 5DWI
- Type
- protein
- Length
- 482 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
- 5G3
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 232 | 70% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 231 | 68% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 56% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5G3 · 4-[(E)-[(2-chlorophenyl)imino](4-hydroxyphenyl)methyl]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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.83 | 0.97 | 24 | 5G3 |
| 2 | 163 | 0.81 | 0.96 | 22 | 5G3 |
| 3 | 90 | 0.62 | 0.89 | 17 | empty |
| 4 | 82 | 0.62 | 0.89 | 17 | empty |
| 5 | 255 | 0.58 | 0.78 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1749 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 462 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DWI · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with a Resorcinyl… · 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 5DWI · PDBe 5DWI · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.