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Crystal structure of the er-alpha ligand-binding domain (L372S, L536S) in complex with dmeri-8
Analyse Crystal structure of the er-alpha ligand-binding domain (L372S, L536S) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RS4
- Type
- protein
- Length
- 977 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- 7I0, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 244 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 246 | 67% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 244 | 68% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 243 | 68% helix, 4% strand | P03372 |
Ligands and binding sites
- 7I0 · (2E)-3-{4-[(1E)-2-(2-chloro-4-fluorophenyl)-1-(2H-indazol-5-yl)but-1-en-1-yl]phenyl}prop-2-enoic acid · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.81 | 0.92 | 27 | 7I0 |
| 2 | 293 | 0.81 | 0.91 | 32 | 7I0 |
| 3 | 283 | 0.79 | 0.90 | 32 | 7I0 |
| 4 | 354 | 0.79 | 0.88 | 37 | 7I0 |
| 5 | 1153 | 0.74 | 0.77 | 106 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1670 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1622 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 406 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (alkylation).
Compared structures
- 7RS4 · Crystal Structure of the ER-alpha Ligand-binding Domain (L372S, L536S) in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P03372 · AlphaFold monomer V2.0 prediction for estrogen receptor (P03372) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 7RS4 · PDBe 7RS4 · UniProt P03372
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