MolNFT v1 · #116589 · protein
Crystal structure of the er-alpha ligand-binding domain in complex with a trifluoro-substituted a-CD ring estrogen derivative (1S,3AR, 5S,7AS)-7A-methyl-5-(2,3,5-trifluoro-4-HYDROXYPHENYL)OCTAHYDRO-1H- inden-1-ol
5DIE · Estrogen receptor: “Crystal structure of the er-alpha ligand-binding domain in complex with a trifluoro-substituted a-CD ring…”. X-ray diffraction, 1 ligand (5CJ), 7 pockets (best druggability 0.84). MolNFT v1 #116589 on GenesisL1…
- PDB
- 5DIE
- Type
- protein
- Length
- 491 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
- 5CJ
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 236 | 65% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 235 | 68% helix, 4% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 10 | 50% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5CJ · (1S,3aR,5S,7aS)-7a-methyl-5-(2,3,5-trifluoro-4-hydroxyphenyl)octahydro-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 | 184 | 0.84 | 0.98 | 22 | 5CJ |
| 2 | 179 | 0.84 | 0.97 | 22 | 5CJ |
| 3 | 88 | 0.64 | 0.90 | 17 | empty |
| 4 | 350 | 0.61 | 0.78 | 37 | empty |
| 5 | 97 | 0.60 | 0.87 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1678 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 503 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5DIE · Crystal Structure of the ER-alpha Ligand-binding Domain in complex with a… · 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 5DIE · PDBe 5DIE · UniProt P03372 · UniProt Q15596
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.