Research workbench
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with lasofoxifene
Analyse Estrogen receptor alpha ligand binding domain Y537S mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VGH
- Type
- protein
- Length
- 456 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- C3D
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 229 | 66% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 227 | 68% helix, 4% strand | P03372 |
Ligands and binding sites
- C3D · (5R,6S)-6-phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.76 | 0.85 | 42 | C3D |
| 2 | 288 | 0.74 | 0.86 | 30 | C3D |
| 3 | 100 | 0.64 | 0.89 | 17 | empty |
| 4 | 85 | 0.60 | 0.88 | 20 | empty |
| 5 | 186 | 0.48 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1544 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6VGH · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant In Complex with Lasofoxifene · 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 0.93
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 6VGH · PDBe 6VGH · UniProt P03372
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