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Crystal structure of the er-alpha ligand-binding domain (L372S, L536S) in complex with dmeri-20
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
- 7RRY
- Type
- protein
- Length
- 890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- L84, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 233 | 72% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 221 | 73% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 227 | 72% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 209 | 71% helix, 4% strand | P03372 |
Ligands and binding sites
- L84 · (1S,2R,4S,5S,6S)-5,6-bis(4-hydroxyphenyl)-N-{4-[3-(piperidin-1-yl)propoxy]phenyl}-N-(2,2,2-trifluoroethyl)-7-oxabicyclo[2.2.1]heptane-2-sulfonamide · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.74 | 0.85 | 25 | L84 |
| 2 | 380 | 0.73 | 0.84 | 33 | L84 |
| 3 | 318 | 0.71 | 0.84 | 31 | L84 |
| 4 | 339 | 0.71 | 0.83 | 31 | L84 |
| 5 | 120 | 0.68 | 0.90 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1577 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1570 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 281 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (alkylation).
Compared structures
- 7RRY · 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 D against A, TM-score 0.95
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 7RRY · PDBe 7RRY · UniProt P03372
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