Research workbench
Crystal structure of the er-alpha ligand-binding domain in complex with the cyclofenil derivative 3-[(E)-(1S,5S)-BICYCLO[3.3.1]NON-9- YLIDENE(4-HYDROXYPHENYL)METHYL]PHENOL
Analyse Crystal structure of the er-alpha ligand-binding domain in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DXM
- Type
- protein
- Length
- 489 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
- 5J0
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 234 | 66% helix, 3% strand | P03372 |
| B | Estrogen receptor | protein | 237 | 65% helix, 2% strand | P03372 |
| C, D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 5J0 · 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.85 | 0.98 | 23 | 5J0 |
| 2 | 204 | 0.84 | 0.96 | 26 | 5J0 |
| 3 | 97 | 0.65 | 0.89 | 16 | empty |
| 4 | 87 | 0.62 | 0.89 | 16 | empty |
| 5 | 165 | 0.49 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1666 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 491 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 463 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5DXM · Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil… · the same entry in another collection · chain B against B, 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 0.99
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 5DXM · PDBe 5DXM · UniProt P03372 · UniProt Q15596
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