Research workbench
Crystal structure of human estrogen receptor alpha ligand-binding domain in complex with a glucocorticoid receptor interacting protein 1 nr box II peptide and estetrol (estra-1,3,5(10)-triene-3,15 alpha, 16ALPHA,17BETA-tetrol)
Analyse Crystal structure of human estrogen receptor alpha ligand-binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L03
- Type
- protein
- Length
- 499 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
- 4OH, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 236 | 71% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 243 | 68% helix, 5% strand | P03372 |
| C | Nuclear receptor coactivator 2 | protein | 11 | 64% helix, 0% strand | Q15596 |
| D | Nuclear receptor coactivator 2 | protein | 9 | 78% helix, 0% strand | Q15596 |
Ligands and binding sites
- 4OH · (14beta,15alpha,16alpha,17alpha)-estra-1,3,5(10)-triene-3,15,16,17-tetrol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.85 | 0.98 | 23 | 4OH |
| 2 | 183 | 0.84 | 0.97 | 22 | 4OH |
| 3 | 391 | 0.63 | 0.78 | 37 | empty |
| 4 | 90 | 0.62 | 0.89 | 20 | empty |
| 5 | 325 | 0.60 | 0.78 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1885 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 554 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 531 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 3L03 · Crystal Structure of human Estrogen Receptor alpha Ligand-Binding Domain in complex with… · 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 3L03 · PDBe 3L03 · UniProt P03372 · UniProt Q15596
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