Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with a para-hydroxyl-substituted, sulfoxide-bridged oxabicyclic heptene sulfonate (sobhs)-2 analog 4-hydroxyphenyl (1S,2S,4S,5S,6R, 7S)-5,6-BIS(4-hydroxy-2-methylphenyl)-7-THIABICYCLO[2.2.1]HEPTANE-2- sulfonate 7-oxide
Analyse Crystal structure of the er-alpha ligand-binding domain in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DUE
- Type
- protein
- Length
- 496 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
- 5FY
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 235 | 68% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 242 | 69% helix, 4% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 10 | 70% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5FY · 4-hydroxyphenyl (1S,2S,4S,7S)-5,6-bis(4-hydroxy-2-methylphenyl)-7-thiabicyclo[2.2.1]hept-5-ene-2-sulfonate 7-oxide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.83 | 0.94 | 31 | 5FY |
| 2 | 303 | 0.83 | 0.93 | 35 | 5FY |
| 3 | 83 | 0.62 | 0.90 | 18 | empty |
| 4 | 73 | 0.60 | 0.89 | 17 | empty |
| 5 | 244 | 0.51 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1683 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 498 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DUE · 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 0.98
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 5DUE · PDBe 5DUE · UniProt P03372 · UniProt Q15596
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