Research workbench
Estrogen receptor alpha ligand binding domain Y537S mutant in complex with stapled peptide SRC2-P5
Analyse Estrogen receptor alpha ligand binding domain Y537S mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DXG
- Type
- protein
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen receptor; Stapled peptide SRC2-P5
- UniProt
- P03372
- Ligands
- EST, NH2
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen receptor | protein | 231 | 68% helix, 4% strand | P03372 |
| B | Estrogen receptor | protein | 222 | 72% helix, 4% strand | P03372 |
| C | Stapled peptide SRC2-P5 | protein | 11 | 45% helix, 0% strand | — |
| D | Stapled peptide SRC2-P5 | protein | 8 | 63% helix, 0% strand | — |
Ligands and binding sites
- EST · Estradiol · ligand · 2 copies · chains A, B
- NH2 · Amino group · ion · chains C
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.84 | 0.98 | 21 | EST |
| 2 | 178 | 0.84 | 0.97 | 23 | EST |
| 3 | 582 | 0.68 | 0.78 | 56 | empty |
| 4 | 109 | 0.63 | 0.87 | 19 | empty |
| 5 | 95 | 0.63 | 0.88 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1601 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 594 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (methylation, nonstandard).
Compared structures
- 5DXG · Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Stapled… · 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 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
- Elsewhere: RCSB PDB 5DXG · PDBe 5DXG · UniProt P03372
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