Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with an methyl-substituted a-CD ring estrogen derivative (1S,3AR,5S, 7AS)-5-(4-hydroxy-2-methylphenyl)-7A-methyloctahydro-1H-inden-1-ol
Analyse Crystal structure of the er-alpha ligand-binding domain in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DI7
- Type
- protein
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Nuclear receptor coactivator 2
- UniProt
- P03372, Q15596
- Ligands
- 5CQ
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 241 | 68% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 245 | 69% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5CQ · (1S,3aR,5S,7aS)-5-(4-hydroxy-2-methylphenyl)-7a-methyloctahydro-1H-inden-1-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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.85 | 0.98 | 22 | 5CQ |
| 2 | 186 | 0.85 | 0.98 | 22 | 5CQ |
| 3 | 100 | 0.65 | 0.89 | 16 | empty |
| 4 | 108 | 0.61 | 0.87 | 18 | empty |
| 5 | 312 | 0.57 | 0.77 | 43 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1653 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 485 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5DI7 · Crystal Structure of the ER-alpha Ligand-binding Domain in complex with an… · 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 A against A, TM-score 0.99
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
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5DI7 · PDBe 5DI7 · UniProt P03372 · UniProt Q15596
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