Research workbench
Estrogen receptor alpha ligand binding domain in complex with bazedoxifene
Analyse Estrogen receptor alpha ligand binding domain in complex with bazedoxifene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XI3
- Type
- protein
- Length
- 918 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- 29S
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 230 | 67% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 233 | 67% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 236 | 66% helix, 3% strand | P03372 |
| D | Estrogen receptor | protein | 219 | 67% helix, 4% strand | P03372 |
Ligands and binding sites
- 29S · Bazedoxifene · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.79 | 0.90 | 37 | 29S |
| 2 | 303 | 0.79 | 0.90 | 30 | 29S |
| 3 | 303 | 0.79 | 0.89 | 34 | 29S |
| 4 | 299 | 0.78 | 0.89 | 31 | 29S |
| 5 | 109 | 0.63 | 0.87 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1454 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1387 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 271 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4XI3 · Estrogen Receptor Alpha Ligand Binding Domain in Complex with Bazedoxifene · 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 0.94
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 4XI3 · PDBe 4XI3 · UniProt P03372
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