Research workbench
Estrogen receptor alpha ligand binding domain in complex with aliphatic serd S-C10(15)
Analyse Estrogen receptor alpha ligand binding domain in complex with aliphatic serd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N9O
- Type
- protein
- Length
- 951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor
- UniProt
- P03372
- Ligands
- 5YR
- Pockets
- 16 · 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 | 239 | 69% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 71% helix, 4% strand | P03372 |
| C | Estrogen receptor | protein | 240 | 68% helix, 4% strand | P03372 |
| D | Estrogen receptor | protein | 237 | 70% helix, 4% strand | P03372 |
Ligands and binding sites
- 5YR · 10-{[3,17beta-dihydroxyestra-1,3,5(10)-trien-7beta-yl]sulfanyl}-N-methyl-N-propyldecanamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.83 | 0.96 | 24 | 5YR |
| 2 | 209 | 0.82 | 0.95 | 27 | 5YR |
| 3 | 222 | 0.82 | 0.94 | 26 | 5YR |
| 4 | 222 | 0.82 | 0.94 | 28 | 5YR |
| 5 | 99 | 0.66 | 0.90 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1649 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1645 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7N9O · Estrogen Receptor Alpha Ligand Binding Domain in Complex with Aliphatic SERD S-C10(15) · 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 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 7N9O · PDBe 7N9O · UniProt P03372
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